|
| Status |
Public on Dec 21, 2018 |
| Title |
H3K27me3_ChIPSeq_Ctrl |
| Sample type |
SRA |
| |
|
| Source name |
416b cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 416b
tissue: bone marrow-derived progenitor cells
cell type: 416b cell line
culture properties: suspension
genotype: Empty vector
|
| Treatment protocol |
416b transduced by PLZF-Flag or empty vector
|
| Growth protocol |
416b cells (Cd34+) were grown in RPMI 10% FCS 1% P/S; GMPs (Lineage negative, C-kit+, Sca-1-, Cd34+, FcγR+) were purified from the different mouse models
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For RNA-seq, total RNA were extracted with RNeasy Plus Mini kit (Qiagen). For ATAC-seq and ChIP-seq home-made protocols were used (see Materials and Methods)
ChIP-seq : MicroPlex Library Preparation Kit (Diagenode) ; ATAC-seq : Nextera DNA Library Prep Kit (Illumina) ; RNA-seq in GMPs : TruSeq Stranded Total RNA with Ribo Zero Gold kit (Illumina) ; RNA-seq in 416b : SMART-Seq v3 Ultra Low Input RNA kit for (Clontech)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
basecalling was performed using Illumina CASAVA
Reads with Phred quality score less than 30 were filtered out
Replicate concurrency was verified by PCA plots, and sample replicates were merged into a single fastq file
Sequences were mapped to a hybride genome (concatenation of mouse and drosophila genome : mm10 and dm6) using Bowtie2 alignment tool (ref: PMID 22388286) with default parameters
Mapped sequences were filtered depending on the organism they belong to
For each mouse datasets, tag counts were normalized by the total number of drosophila mapped tags such that each file correspond to the same amount of drosophila reads.
bigwig files were generated from spiked in bam files using either a customed script or Deeptools 2.0 suite (bamCompare)
Peak callings were performed using MACS2 (in sharp mode for transcription factors; in broad mode for histone marks) using inputs as controls
Genome_build: mm10
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Dec 21, 2018 |
| Contact name |
Mathilde Poplineau |
| E-mail(s) |
[email protected]
|
| Organization name |
INSERM
|
| Street address |
27 BOULEVARD LEI ROURE CS 30059
|
| City |
Marseille |
| ZIP/Postal code |
13273 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE124190 |
PLZF limits enhancer activity during hematopoietic progenitor aging |
|
| Relations |
| BioSample |
SAMN10620510 |
| SRA |
SRX5170150 |
