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| Status |
Public on Dec 01, 2019 |
| Title |
GSTS_005: JRy12376-12377_mixed_strepSeq_cycling |
| Sample type |
SRA |
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| Source name |
mixed cycling cultures of JRy12376, 12377 ex vivo and precipitated chromatin with streptavidin
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JRy12376, JRy12377
growth conditions: fixed in exponential phase, mixed ex vivo
genotype: H3-Avi TetR-BirA(1-213); H3-Avi TetR-BirA(214-320) gal10::TetO
preciptation conditions: streptavidin (invitrogen #65001)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were mechanically disrupted, and chromatin was solubilized with Mnase. Chromatin was precipitated using either streptavidin-coupled magnetic beads or a V5 antibody agarose matrix.
NEBNext Ultra II library kit was used with dual index primers to prepare DNA for sequencing
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiniSeq |
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| Description |
fig panel: 1b,c
GSTS_005
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| Data processing |
Raw reads were mapped to SacCer3 reference genome, modified to include the gal10::TetO sequence. Sequences were aligned using Bowtie2 with parameters -p 16 -N 1 -L 17, and raw reads were trimmed to 38bp for all experiments.
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, each base in the genome was counted for how often it appeared in the sequencing library (NOT how often the base was sequenced, but rather how often each base fell between the ends of a concordantly-aligned paired ned read).
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, read midpoints were extracted and stored as a bedGraph, corresponding to a histogram of read midpoints
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: All proccessed data is a BedGraph
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| Submission date |
Jul 30, 2019 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Gavin Schwebs Schlissel |
| E-mail(s) |
[email protected]
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| Phone |
9256428068
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| Organization name |
UC Berkeley
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| Department |
Molecular Cell Biology
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| Lab |
Rine
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| Street address |
440 Barker Hall
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL22715 |
| Series (1) |
| GSE135102 |
The nucleosome core particle remembers its position through DNA replication and transcription |
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| Relations |
| SRA |
SRX6614921 |
| BioSample |
SAMN12413019 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3985934_JRy12376-12377-mixed_S7_L001_R1_001.fastq.gz.sam.bedGraph.gz |
57.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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