|
| Status |
Public on Mar 01, 2020 |
| Title |
Setd8-null Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
primitive erythroblasts
|
| Organism |
Mus musculus |
| Characteristics |
embryonic day: E10.5
tissue: Peripheral Blood
genotype: setd8-null
|
| Treatment protocol |
Primary cells not treated ex vivo. Cells were stained for flow cytometry on ice in PBS supplemented with glucose and BSA
|
| Growth protocol |
Primary cells not subjected to ex vivo culture
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Primitive erythroblasts were removed from peripheral blood by dissection in PBS supplemented with glucose and BSA
Briefly, nuclei were collected from Setd8 null and control erythroblats following cell lysis and subjected to tagmentation using transpoase (Ilumina Nextera FC121-1030). Samples were then amplified x 5 PCR cycles [980C/45s + 5 x (980C/15s + 630C/30s + 720C/30s) + 720C/1min] using KAPA HiFi HotStart ReadyMix PCR Kit (KK2601/KK2602) and cleaned with Qiagen MiniElute column. The library was then amplified with PCR [980C/45s + Y x (980C/15s + 630C/30s + 720C/30s) + 720C/1min], with the number of cycles (Y) determined through via a qPCR library amplification test. The resulting PCR producte was cleaned using Agencourt AMPure XP magnetic beads (Beckman Coulter A63880)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
setd8-mutant_peaks.narrowPeak
setd8-mutant_ratio.bw
log2ratio_readCountNorm_mutant_vs_control.bw
|
| Data processing |
bcl2fastq to convert reads to fastq format
trimmomatic was used to perform quality control (SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP: trimmomatic_adapters.fasta:2:30:10 MINLEN:15
quality reads were aligned using bowtie1 -m 1
mitochonrial reads and blacklist reads were removed using samtools
significantly accessible regions were identified using MACS2 --nomodel --shift -100 --extsize 200 -f BAM -B -g mm
replicate bam files were merged using samtools
deeptools bamCompare was used to compute the log2 ratio between setd8-null and control read density while applying sequencing depth normalization
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak, bigwig
|
| |
|
| Submission date |
Sep 27, 2019 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Laurie A Steiner |
| E-mail(s) |
Laurie_Steiner@urmc.rochester.edu
|
| Organization name |
University of Rochester
|
| Department |
Center for Pediatric Biomedical Research
|
| Lab |
Steiner Lab
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE138106 |
The histone methyltransferase Setd8 alters the chromatin landscape and regulates the expression of key transcription factorsduring erythroid differentiation |
|
| Relations |
| BioSample |
SAMN12861962 |
| SRA |
SRX6916352 |
