|
| Status |
Public on Aug 15, 2023 |
| Title |
polyA-RNA-seq for chALL patient sample 3 |
| Sample type |
SRA |
| |
|
| Source name |
MLL-AF4 childhood ALL patient 3 blasts
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: acute lymphoblastic leukemia (ALL)
treatment: N/A
individual: 3-year old MLL-AF4 ALL patient
tissue: Bone marrow aspirate
|
| Growth protocol |
Infant (<1 year old) and childhood ALL samples were obtained from Blood Cancer UK Childhood Leukemia Cell Bank, UK (REC: 16/SW/0219). All ALL samples were anonymized at source, assigned a unique study number and linked. Cryopreserved samples were thawed, and immediately processed.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from 1 million cells using the RNeasy mini kit (Qiagen). Poly A purification was conducted using the NEB Poly(A) mRNA magnetic isolation module as per the manufacturer’s protocol.
cDNA libraries were prepared using the NEB Next Ultra II Directional RNA library preparation kit for Illumina (E7760).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
chALL3
|
| Data processing |
RNA-seq reads were aligned to the hg19 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using edgeR
Assembly: hg19
Supplementary files format and content: CPMs
|
| |
|
| Submission date |
May 07, 2022 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Thomas A Milne |
| E-mail(s) |
thomas.milne@imm.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
MRC Weatherall Institute of Molecular Medicine
|
| Street address |
John Radcliffe Hospital, Headington
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE202447 |
MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia [RNA-seq] |
| GSE202451 |
MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia |
|
| Relations |
| BioSample |
SAMN28131847 |
| SRA |
SRX15203351 |
