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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 22, 2020 |
| Title |
E16Ezh1hetEzh2null-2 |
| Sample type |
SRA |
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| Source name |
Embryonic Kidneys
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: E16.5
genotype: Ezh1+/- ; Six2TGCEzh2-/-
strain: 129 * C57BL/6
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Corces et al., 2017
Buenrostro et al., 2013
Omni-ATAC
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
Ezh1+/- Six2TGCEzh2-/- NPCs
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| Data processing |
Concatenate paired-end reads run across multiple lanes for each sample such that there exist one forward (_1.fastq.gz) and one reverse (_2.fastq.gz) reads file for each sample.
Assess quality of reads using FASTQC(v0.11.7)
Aligned paired-end Fastq files to mm10 using Bowtie2
Samtools to remove Mitochondrial reads
Picard tools v1.77 to remove Duplicates
Call narrow peaks using MACS2
Bedtools to generate sorted bdg and bigwig files for viewing in IGV
mm10
Bigwig files
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| Submission date |
Jan 28, 2020 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Samir S El-Dahr |
| E-mail(s) |
seldahr@tulane.edu
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| Organization name |
Tulane University
|
| Department |
Pediatric Nephrology
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| Lab |
5534 School of Medicine
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| Street address |
1430 Tulane Avenue
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| City |
New Orleans |
| State/province |
Louisiana |
| ZIP/Postal code |
70112 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE144384 |
Polycomb proteins, Ezh1 and Ezh2, co-regulate chromatin accessibility and nephron progenitor cell lifespan |
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| Relations |
| BioSample |
SAMN13937169 |
| SRA |
SRX7643551 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4287200_E16Ezh1hetEzh2null-2_nPN_treat_pileup.bdg.scaled1000.bw |
164.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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