|
| Status |
Public on Aug 16, 2021 |
| Title |
IgG 15000 cell [CUT&RUN] |
| Sample type |
SRA |
| |
|
| Source name |
E10.5 yolk sac erythro-myeloid progenitors
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E10.5
strain: C57BL/6
genotype/variation: Ezh2fl/fl; Tie2-Cre+/+ Wild type
tissue: yolk sac
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
E10.5 yolk sac erythro-myeloid progenitors were prepared for CUT&RUN using the CUT&RUN kit from Cell Signaling Technologies with Rabbit (DA1E) mAb IgG XP® isotype control (Cell Signaling Technologies) and anti-H3K27me3 (07-449, Merck MilliPore).
DNA libraries were pre-amplified using 17 (500 EMPs) or 16 (15,000 EMPs) cycles of PCR. DNA libraries were prepared using Nextera XT (Illumina). Samples were sequenced using the Illumina NextSeq 550 (500 EMPs) and NovaSeq XP (15,000 EMPs) platform, generating 76 bp (500 EMPs) and 59 bp (15,000 EMPs) paired-end reads.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were mapped to the mouse reference genome (GRCm38) with bowtie2 (version 2.2.1)
Parameter for bowtie2 mapping were: --dovetail --phred33
Samtools (version 1.9) was used to convert SAM files to BAM files
Peaks was called using MACS2 (version 2.1.2)
Parameters used for MACS2 peak calling: --broad --pvalue 0.01 (for the 10k cell) or --pvalue --0.01 (for the 500 cell sample)
Deeptools (version 3.5.1) was used to convert BAM to bigWig
Parameters used for deeptools BAM to BigWig conversion: bamCoverage --bam ${bamDir} -o ${outDir} --normalizeUsing None --effectiveGenomeSize 2150570000 --extendReads --ignoreForNormalization chrX --binSize 10
Genome_build: mm10
Supplementary_files_format_and_content: BED: Peaks called by MACS2, bigWig: Coverage tracks from deeptools bamCompare. Annotated BED: Annotated BED from from ChIPpeakAnno
|
| |
|
| Submission date |
Aug 11, 2021 |
| Last update date |
Aug 17, 2021 |
| Contact name |
Georges Lacaud |
| E-mail(s) |
georges.lacaud@cruk.manchester.ac.uk
|
| Organization name |
Cancer Research UK Manchester Institute
|
| Department |
Stem Cell Biology
|
| Street address |
Alderley Park
|
| City |
Alderley Edge |
| State/province |
England |
| ZIP/Postal code |
SK10 4TG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE181869 |
Ezh2 is essential for the generation of functional yolk sac derived erythro-myeloid progenitor [CUT&RUN] |
| GSE181873 |
Ezh2 is essential for the generation of functional yolk sac derived erythro-myeloid progenitors. |
|
| Relations |
| BioSample |
SAMN20708755 |
| SRA |
SRX11716908 |
