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| Status |
Public on Mar 13, 2024 |
| Title |
B10_K27me3_R3 |
| Sample type |
SRA |
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| Source name |
C3H/10T1/2 (CCL-226) cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: C3H/10T1/2 (CCL-226) cells
cell type: mesenchymal progenitor cells
genotype: Atrx knockout
chip antibody: H3K27me3(CST9733)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For histone marks, cells were collected by trypsin. Washed by PBS. For ATRX, cells were gently fixed using 0.1% PFA in PBS for 1 min at room temperature, followed by nuclei extraction with NE buffer (20 mM HEPES (pH7.9), 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 1 mM MnCl2, 1×cOmplete Mini-Tablet (1 tablet), 0.5 mM Spermidine) according to the protocol from EpiCypher.
Libraries were generated using NEBNext Ultra II kits.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Cut and run reads were aligned using Rsubread’s align method and predicted fragment lengths were calculated by the ChIPQC R Bioconductor package. Normalized, fragment extended signal bigWigs were created using the rtracklayer R Bioconductor package. Peak calls were made using the SEACR software.
Assembly: mm10
Supplementary files format and content: bigwig files normalized to read depth
Supplementary files format and content: bed files generated by SEACR
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| Submission date |
Aug 03, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Douglas Barrows |
| E-mail(s) |
dbarrows@rockefeller.edu
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| Phone |
7749940981
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| Organization name |
Rockefeller University
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| Street address |
1230 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE240028 |
ATRX guards against aberrant differentiation in mesenchymal progenitor cells (CUT&RUN) |
| GSE240030 |
ATRX guards against aberrant differentiation in mesenchymal progenitor cells |
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| Relations |
| BioSample |
SAMN36829050 |
| SRA |
SRX21240714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7680109_Sorted_B10_k27me3_R3Normalised.bw |
172.6 Mb |
(ftp)(http) |
BW |
| GSM7680109_stringent_0.01_B10_k27me3_R3.stringent.bed.gz |
535.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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