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Sample GSM2463193 Query DataSets for GSM2463193
Status Public on Jul 17, 2017
Title WT Ssb2 interactome, replicate 1
Sample type SRA
 
Source name Yeast
Organism Saccharomyces cerevisiae
Characteristics strain: BY4741
genotype: Ssb2-GFP::kanMX4
Treatment protocol Cultures were filtered, flash frozen and lysed in frozen state using a mixer mill. Ribosomes were pelleted through a sucrose cushion and resuspended. From this a part was used for RNA extraction (total RNCs) and the rest was used to purify GFP-tagged Ssb using a GFP-antibody coupled to sepharose-beads (Ssb-bound RNCs).
Growth protocol Cultures were grown in YPD at 30°C and 150 rpm
Extracted molecule total RNA
Extraction protocol RNA was extracted using the hot acid phenol method (for details see Becker et al. 2013)
DNA libraries were generated following previously published protocoles (Ingolia et al. 2009, Becker et al. 2013)
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Library strategy: Ribosome profiling
Barcode and linker removal using Cutadapt 1.11
Alignment to rRNA using Bowtie2.2.5.0
Alignment to genome using TopHat2.0.13
center weighting of ribosomal footprints (custom python script)
normalization to total read number per sample (custom python script)
Genome_build: NCBI build3.1
Supplementary_files_format_and_content: NormReads-files: column1: chromosome number, column2: nt position, column3: center weighted reads on plus strand, column4: center weighted reads on minus strand, column5: normalized reads on plus strand, column6: normalized reads on minus strand
 
Submission date Jan 19, 2017
Last update date May 15, 2019
Contact name Kristina Döring
E-mail(s) k.doering@zmbh.uni-heidelberg.de
Organization name Heidelberg University
Department ZMBH
Lab Bernd Bukau
Street address Im Neuenheimer Feld 282
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL13821
Series (1)
GSE93830 Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding
Relations
BioSample SAMN06241931
SRA SRX2504525

Supplementary file Size Download File type/resource
GSM2463193_KD16_WSandNormReads.txt.gz 67.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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