|
| Status |
Public on Jun 27, 2022 |
| Title |
H3K27ac_proB_WT_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
pro-B lymphocyte
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pro-B lymphocyte
genotype: wild-type
chip antibody: H3K27ac #ab4729
|
| Treatment protocol |
HDAC7 knockout cells have a floxed Hdac7 and a CRE
|
| Growth protocol |
Cells were extracted from fresh murine bone marrow and sorted to obtain purified pro-B and pre-B cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Murine proB and preB lymphocytes were fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer. DNA sequencing libraries were prepared using the TRUESEQ ChIP kit (Illumina). Libraries were sequenced using HiSeqX 150+150PE platform from Magrogene Inc.
Libraries were constructed using TRUSEQ ChIP kit from Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Reads were aligned to mm10 using Bowtie v2.3.2
Filtering was based on ENCODE standards and removed those mapping to the blacklist and duplicates using samtools (v.1.9) and sambamba (v.0.7.0)
For peak calling MACS2 v2.2.7.1 was used
narrowPeak or broadPeak files were generated using MACS v2 with default settings
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (for H3K27ac) and broadpeak (for H3K27me) and excepting input samples
|
| |
|
| Submission date |
May 24, 2022 |
| Last update date |
Jun 27, 2022 |
| Contact name |
Maribel Parra |
| E-mail(s) |
mparra@carrerasresearch.org
|
| Organization name |
Josep Carreras Leukaemia Research Institute
|
| Department |
Lymphocyte Development and Disease
|
| Lab |
2.30
|
| Street address |
Ctra. de Can Ruti, Camà de les Escoles, s/n
|
| City |
Badalona |
| State/province |
Barcelona |
| ZIP/Postal code |
08916 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE204673 |
The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development [ChIP-seq] |
| GSE204674 |
The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development |
|
| Relations |
| BioSample |
SAMN28631595 |
| SRA |
SRX15432236 |
