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| Status |
Public on Feb 07, 2023 |
| Title |
Rpb1ChIP_dcp2_Replicate_2 |
| Sample type |
SRA |
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| Source name |
Whole cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: W303 F2150 (MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 dcp2delta-::HIS3)
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| Growth protocol |
In additional columns of the SAMPLES section
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, for ChIP assays, chromatin was prepared from formaldehyde-crosslinked cells, immunoprecipitated with Rpb1 antibodies, and the DNA was extracted . DNA libraries for Illumina paired-end sequencing were prepared using DNA Library Prep Kit for Illumina from New England Biolabs
In additional columns of the SAMPLES section
In additional columns of the SAMPLES section
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For RNA-Seq: As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
For ChIP-Seq: Sequence data were aligned to the SacCer3 version of the genome sequence using Bowtie2 with parameters -X 1000 -very-sensitive, to map sequences up to 1 kb with maximum accuracy. PCR duplicates from ChIP-seq data were removed using the samtools rmdup package.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For RNA-Sequencing, each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads. For Rpb1 ChIP-Seq, average occupancy file contains five columns providing: systemmatic gene name (ORF), avg occupancy at -1, NDR, +1 and average of -1, NDR, +1
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| Submission date |
Dec 08, 2022 |
| Last update date |
Feb 07, 2023 |
| Contact name |
Alan G Hinnebusch |
| E-mail(s) |
[email protected]
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| Organization name |
National Institutes of Health
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| Department |
Eunice Kennedy Shriver National Institute of Child Health and Human Development
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| Lab |
Section on Nutrient Control of Gene Expression
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| Street address |
6 Center Drive
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL27812 |
| Series (1) |
| GSE220578 |
Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability II |
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| Relations |
| BioSample |
SAMN32118009 |
| SRA |
SRX18543687 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6807056_Avg_occ_Rpb1ChIP_dcp2_Replicate_2.csv.gz |
184.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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