|
| Status |
Public on Dec 27, 2022 |
| Title |
M13-SAFB-Cr-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF9 positive MOLM13
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MLL-AF9 positive MOLM13
cell type: AML cell line
treatment: CRISPR-ko-SAFB
|
| Treatment protocol |
--
|
| Growth protocol |
--
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using RNeasy Plus mini (QIAGEN) kit following manufacturer’s instructions.
libraries were prepared using Illumina kit (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, Cat# E7760S) with RiboZero depletion following manufacturer’s instructions. Libraries were sequenced on Hiseq platform with PE150 reads length.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired end RNA-seq reads were quality filtered and adapter sequences were trimmed using TrimGalore package.
Trimmed sequence reads were mapped using STAR version=2.7.10a against the human genome (Hg38). Uniquely-mapping, high confidence reads were retained using the following flags (NH:i:1 and MAPQ=255).
Read counts were quantified with HTSeq version 1.99.2
Assembly: hg38
Supplementary files format and content: BigWig files of uniquely mappable, high-confidence reads for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig
Supplementary files format and content: tab-delimited text files containing read counts for each gene (in ENSEMBL IDs)
|
| |
|
| 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) |
| GSE221700 |
HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia [RNA-seq] |
| GSE221701 |
HOXA9 forms a repressive complex with nuclear matrix-associated protein SAFB to maintain acute myeloid leukemia |
|
| Relations |
| BioSample |
SAMN32388978 |
| SRA |
SRX18840610 |
