|
| Status |
Public on Dec 27, 2022 |
| Title |
AML#4-Input |
| Sample type |
SRA |
| |
|
| Source name |
primary AML cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: untreated
cell type: primary AML cells
genotype: FLT3+CBFB
chip antibody: none
|
| Treatment protocol |
--
|
| Growth protocol |
--
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using CUTANA CUT&RUN kit (Epicypher) following manufacturer’s instructions. 100,000 MOLM13 cells were used for the assay for each antibody.
Libraries were prepared using 2ng of DNA using NEBNext UltraII DNA library preparation kit (Cat# E7645S, Illumina) and Dual index primer-Multiplex Oligos (Cat# E7600S, Illumina).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For ChIP-seq data, paired end reads were quality checked and adapter sequences were trimmed using TrimGalore package. CUT&RUN libraries were analysed using CUT&RUNTools v2.0 pipeline with default parameters.
ChIP-seq reads were aligned against human reference genome (Hg38) using Bowtie2.
Uniquely mapped reads were retained and peaks were called uing MACS v2 against input controls with the significance cut-off q-value (FDR) < 0.1/0.05.
Peaks were further filtered by removing blacklisted regions from Encode
Assembly: hg38
Supplementary files format and content: BigWig files of reads, normalised to counts-per-million (cpm) or scaled by library size, for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig.
Supplementary files format and content: narrowPeak (except for Input files) files generated by MACS2 against input controls at p-value 0.05 and FDR (q) values 0.05-0.1
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Dec 23, 2022 |
| Last update date |
Dec 27, 2022 |
| Contact name |
George Giotopoulos |
| Organization name |
University of Cambridge
|
| Department |
Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology
|
| Lab |
Brian Huntly
|
| Street address |
Jeffrey Cheah Biomedical Centre, Puddicombe Way
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 0AW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE221697 |
HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia [CUT&RUN/ChIP-Seq] |
| GSE221701 |
HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN32388911 |
| SRA |
SRX18840446 |
