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| Status |
Public on Mar 21, 2024 |
| Title |
MLVQ15 |
| Sample type |
SRA |
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| Source name |
Chromatin extrated after immunoprecipitation with various antibodies.
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| Organism |
Mus musculus |
| Characteristics |
tissue: Skeletal muscle
strain: C57BL/6J
age: 10 weeks
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
P2731
P2727 AND 2731: ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 2-20 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents. , P2731 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 1-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
LSD1 24h starved
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Assembly: mm10
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| Submission date |
Apr 25, 2023 |
| Last update date |
Mar 21, 2024 |
| Contact name |
Delphine Duteil |
| E-mail(s) |
duteild@igbmc.fr
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| Organization name |
IGBMC
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| Street address |
1 rue Laurent Fries
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| City |
ILLKIRCH |
| ZIP/Postal code |
67400 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (2) |
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| Relations |
| BioSample |
SAMN34369144 |
| SRA |
SRX20097265 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7226648_24h_Lsd1_20752.bed.gz |
1.4 Mb |
(ftp)(http) |
BED |
| GSM7226648_24h_Lsd1_20752_limb_MLVQ15.bigwig |
168.9 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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