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| Status |
Public on May 24, 2023 |
| Title |
H3.1_cleavable_II_HA |
| Sample type |
SRA |
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| Source name |
mESC
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| Organism |
Mus musculus |
| Characteristics |
chip antibody: HA
cell type: mESC
sensor type: cleavable H3.1
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Crosslinked pellet was re-suspended in 20ul of cell lysis buffer (50mM Tris pH8.0, 150mM NaCl, 1%TritonX-100, 0.1%sodium deoxycholate, 5 mM CaCl2, EDTA-free protease inhibitor cocktail and incubated on ice for 15 minutes. Cells were centrifuged at 3000RPM for 10 minutes at 4°C. The supernatant was discarded, and pellet was re-suspended in 10ul of lysis buffer supplemented with 17.5 units of micrococcal nuclease (Worthington MNase, LS004798) and chilled on ice for 10 minutes. Samples were incubated at 37°C for 15 minutes. To stop reaction, 20mM EDTA was added and samples were vortexed and placed on ice for 30 minutes. Cell lysate was then centrifuged at max speed (20,000xg) for 10 minutes at 4°C and supernatant moved to a separate tube. Reaction volume was increased to 180ul with RIPA buffer (10mM Tris pH8.0, 140mM NaCl, 1mM EDTA, 0.1%SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail), and reaction was then split into two separate wells of 96-well LoBind Eppendorf plate. ~5ug of anti-HA (12CA5) and anti-myc (9E10) antibodies was added to the separate wells and incubated at 4°C for 2 hours with rotations. Both antibody stocks were the supernatant of the respective hybridoma cell cultures grown in miniPERM bioreactors in-house by the Weizmann Institute Core Facility Antibody Unit. All subsequent steps were carried out as described in (Gutin et al., 2018).
SLIM-Chip, as per Gutin et al, Cell Reports 2019
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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 |
Paired-end reads were aligned to the mm10 genome assembly downloaded from the UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest using bowtie2 with default options.
Aligned files were then imported into R with readGAlignments function from GenomicAlignments package (Lawrence et al., 2013), requiring minimum mapping quality of 10.
bw fille was created using bamCoverage command from deepTools package with the following options: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --maxFragmentLength 300
Assembly: mm10
Supplementary files format and content: bw
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| Submission date |
Oct 04, 2022 |
| Last update date |
May 24, 2023 |
| Contact name |
Yonatan Stelzer |
| E-mail(s) |
yonatan.stelzer@weizmann.ac.il
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| Organization name |
Weizmann Institute of Science
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| Street address |
Herzl 234
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| City |
Rehovot |
| State/province |
Israel |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE213076 |
Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN31149503 |
| SRA |
SRX17793739 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6615290_H3.1_cleavable_II_HA.bw |
612.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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