|
| Status |
Public on Feb 17, 2017 |
| Title |
1Snf5Snf2IP (ChIP-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
1Snf5Snf2IP
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: Snf5 deletion
sample extract: WCE
chip antibody: Snf2 C' Ab (antibody raised in Reese lab)
|
| Treatment protocol |
Cells were grown in YPD to Abs ~0.8 and crosslinked for ChIP and Mnase, harvested without crosslinking for isolating RNA
|
| Growth protocol |
Cells were grown in YPD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Yeast whole cell extract were sonicated DNA-protein complexes were isolated with Snf2-C'antibody (kind gift from Joseph Reese Pennsylvania State University: antibody raised in Reese lab) .
ChiP-seq, Mnase-seq, RNA-seq libraries were prepared using KAPA High Throughput Library Preparation Kit, Roche.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina data was processed for all samples with RTA 1.17.21.3 and CASAVA 1.8.2 from Illumina.
ChIP-seq data was aligned to sacCer2 genome from UCSC with bowtie2 (2.1.0) with -k 1.
MNase-seq paired-end data was aligned to sacCer2 with bowtie2 (2.1.0). Same-fragment reads from fragments sized between 100 and 200 were centered at their midpoint and resized to the 73 middle bases, then normalized to reads per million for the bigWig files.
RNA-seq data was aligned to sacCer2 with a gtf file from Ensembl 63 using tophat (2.0.10) with --segment-mismatches 1 -x 1 -g 1 --no-coverage-search.
Any downstream analysis and bigWig file generation was done in R.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig files were created in all cases by reading in bam files, normalizing to reads per million by multiplying by 1 million and dividing by the total number of alignments. For RNA-seq (strand specific protocol), data was split into positive (forward) and negative (reverse) strands for the bigWIg files.
|
| |
|
| Submission date |
May 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17342 |
| Series (1) |
| GSE81722 |
Composition and Function of Mutant Swi/Snf Complexes |
|
| Relations |
| BioSample |
SAMN05162313 |
| SRA |
SRX1791121 |
