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| Status |
Public on Jun 24, 2020 |
| Title |
CENP-A_ChIP_rep3 |
| Sample type |
SRA |
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| Source name |
Red Blood Cells
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| Organism |
Xenopus laevis |
| Characteristics |
strain: J-strain
cell type: Red Blood Cells
chip antibody: X. laevis Rb-anti-CENP-A (Straight)
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| Treatment protocol |
no treatement conditions
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from cells through dounce nuclear extraction, incubated with MNase (300U 30min RT). Soluble mononucleosomes were extracted and precleared prior to use as input for antibody pulldowns.
Sequencing libraries were prepared with the NEBNext Ultra II DNA Library prep kit (E7645) with up to 1µg of input or ChIP eluate DNA following the manufacturer’s protocol
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Remove PCR duplicates with BBtools Clumpify, bbmap v38.06
Trim adapters with trimmomatic, v0.38
Generate k-mers with KMC, v3.1.1
Identify CENP-A enriched k-mers
Align genome segments with enriched k-mers with bowtie2 v2.3.5
Align enriched k-mers with bowtie v1.2.2 with parameters -v 0 -a
Generate, sort ,index bam with Samtools, v1.9
Generate bigWig with deeptools, v2.5.7, -bs 5
Genome_build: X. laeivs v10.3
Supplementary_files_format_and_content: bigWig displaying mapping of CENP-A enriched k-mers
Supplementary_files_format_and_content: xla_v10.2_cen.bed: Bed file from the CENP-A ChIP dataset used in the analysis.
Supplementary_files_format_and_content: FCR_monomers.fa: FASTA file from the CENP-A ChIP dataset used in the analysis.
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| Submission date |
Jun 23, 2020 |
| Last update date |
Nov 25, 2020 |
| Contact name |
Owen Kabnick Smith |
| E-mail(s) |
smithok@stanford.edu
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| Organization name |
Stanford University School of Medicine
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| Department |
Biochemistry
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| Lab |
Straight
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| Street address |
279 Campus Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL22426 |
| Series (1) |
| GSE153058 |
Identification and characterization of centromeric sequences in Xenopus laevis |
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| Relations |
| BioSample |
SAMN15351295 |
| SRA |
SRX8602697 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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