|
| 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 |
