|
| Status |
Public on Sep 08, 2022 |
| Title |
CLL_empty vector_H3K27ac [P1] |
| Sample type |
SRA |
| |
|
| Source name |
Primary CLL cells
|
| Organism |
Homo sapiens |
| Characteristics |
patient: P1
diagnosis: Chronic lymphocytic leukemia
cell type: Primary CLL cells from peripheral blood
genotype/variation: Control
chip antibody: H3K27ac antibody, Diagenode: C15410196 /pAb-196-050 (LOT: A1723-0041D)
|
| Treatment protocol |
Cells were crosslinked with 1% formaldehyde, 15 minutes at 4ยบ. Reaction was stopped with 1.25 M glycine for 5 minutes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq were generated as described: http://www.blueprint-epigenome.eu/index.cfm?p=7BF8A4B6-F4FE-861A-2AD57A08D63D0B58
Libraries were constructed using the Kapa Hyper Prep Kit as previously described (https://www.blueprint-epigenome.eu/UserFiles/File/Protocols/Blueprint_Kapa_hyper_prep_kit.pdf).
SE, 50bp
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
P1_CNT
|
| Data processing |
Raw fastq files alignment using bwa 0.7.7, picard & samtools.
Wiggle plots generation using PhantomPeakQualTools.
Narrow peak calling using MACS2 callpeak function with q-value < 0.01 and without input control.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: *.bed: Bed files describing the location of the peaks.
|
| |
|
| Submission date |
Feb 13, 2021 |
| Last update date |
Sep 08, 2022 |
| Contact name |
Irina Mohorianu |
| E-mail(s) |
data-submissions@stemcells.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Wellcome-MRC Cambridge Stem Cell Institute
|
| Street address |
Puddicombe Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE150610 |
Gene expression profile of primary CLL cells transduced with a mutated NOTCH1 |
| GSE166727 |
Histone H3 lysine 27 acetylation (H3K27ac) profile of primary CLL cells transduced with a retrovirus expressing mutated NOTCH1 |
|
| Relations |
| BioSample |
SAMN17910351 |
| SRA |
SRX10095003 |
