|
| Status |
Public on Jan 12, 2017 |
| Title |
SEM_NascentRNASeq_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Leukemia cell line (SEM)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Leukemia cell line; SEM
cell type: Paediatric pro B-cell line derived from ALL with t(4;11)(q21;q23) translocation
molecule subtype: nascent RNA
|
| Growth protocol |
SEM cells were continuously grown in IMDM with 10-20% FBS, split when they reached a density of 1-2X10e6 down to 5X10e5; all other cell lines were grown in a similar manner in RPMI 1640.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP-seq: Fixed cells were lysed in 1% SDS lysis buffer. Samples were sonicated and protein-DNA complexes were isolated with antibody.
Nascent RNA-seq: 108 4sU-treated cells were lysed in 10ml Trizol. RNA was extracted using chloroform and precipitated with EtOH. 4sU RNA was biotinylated with 1mg/ml Biotin-HPDP and nascent RNA was enriched for using streptavidin-coated beads.
Libraries were prepared according to Illumina's protocol accompanying the DNA Library Prep Master Mix Set (Part# E6040) or Ultra RNA Library Prep Master Mix Set (Part# E7530).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file: SEM_nascent_rpkm_table.txt
|
| Data processing |
ChIP-seq reads were aligned to the hg18 genome using bowtie version 1.1.2 with following parameters: p1 m2 best strata sam
Peaks were called using SeqMonk version 0.24.1
Nascent RNA-seq reads were aligned to the hg18 genome using STAR
Read counts were determined using featureCounts (Subread package)
Genome_build: hg18
Supplementary_files_format_and_content: bed files were generated from text files outputted directly from SeqMonk; Rpkm tables (.txt) were generated using edgeR
|
| |
|
| Submission date |
Jun 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Milne |
| E-mail(s) |
thomas.milne@imm.ox.ac.uk
|
| Organization name |
Weatherall Institute of Molecular Medicine
|
| Department |
Molecular Haematology Unit
|
| Street address |
John Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE83671 |
MLL-AF4 Spreading Identifies Binding Sites that Are Distinct from Super-Enhancers and that Govern Sensitivity to DOT1L Inhibition in Leukemia. |
|
| Relations |
| BioSample |
SAMN05290471 |
| SRA |
SRX1873459 |
