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Transcriptional and DNA binding profiling of CEBPE in REH acute lymphoblastic leukaemia cells using shRNA RNA-Seq and ChIP-Seq

ChIP-Seq - CEBPE - REH. The ETV6/RUNX1 translocated acute lymphoblastic leukaemia cell line. REH was used to perform ChIP-Seq using a CEBPE antibody. Cells were fixed in 1% formaldehyde for 10mins, prior to preparation of chromatin using Active Motif Express ChIP-IT. 2ug of antibody (anti CEBPE Atlas Antibodies HPA002928)was added to 25ug of chromatin O/N at 4C with rotation. Duplicate reactions were pooled and purified. 10ng of ChIP’d and input DNA used for Illumina NGS preparation (NEBNext ChIP-Seq Library kit; New England Biolabs), CEBPE and Input DNA ChIP samples were sequenced on a MiSeq using 150bp Kit v3 paired end and a HiSeq 2500 using 2x101 version 4 paired end (Illumina) respectively. Reactions performed in duplicate. shCEBPE RNA-Seq - REH. REH cells were lentivirally transduced with a pTRIPZ shRNA vector for transcriptional profiling of CEBPE. Two controls (empty and non-targeting) and two CEBPE shRNAs (V3THS_150517(A13), V3THS_404312(G3) Dharmacon, GE) were transduced into REH cells. Cells were treated with 1ug/ml doxycyclin for 144hrs and total RNA purified using Qiagen RNeasy. Knock down of CEBPE was validated by qRT. RNA integrity >7.7 for all samples. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit and sequenced on an Illuimna HiSeq 2500 using 2x101 version 4 paired end chemistry. 3 biological replicates of each samples were prepared.

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Data release policy of transcriptional and DNA binding profiling data of CEBPE in REH acute lymphoblastic leukemia cells

All data will be available on publication

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001002877 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00001996500 fastq.gz 1.5 GB
EGAF00001996501 fastq.gz 1.5 GB
EGAF00001996502 fastq.gz 1.5 GB
EGAF00001996503 fastq.gz 1.5 GB
EGAF00001996504 fastq.gz 1.8 GB
EGAF00001996505 fastq.gz 1.8 GB
EGAF00001996506 fastq.gz 2.7 GB
EGAF00001996507 fastq.gz 2.8 GB
EGAF00001996508 fastq.gz 2.9 GB
EGAF00001996509 fastq.gz 2.9 GB
EGAF00001996510 fastq.gz 2.8 GB
EGAF00001996511 fastq.gz 2.8 GB
EGAF00001996512 fastq.gz 2.2 GB
EGAF00001996513 fastq.gz 2.3 GB
EGAF00001996514 fastq.gz 2.3 GB
EGAF00001996515 fastq.gz 2.4 GB
EGAF00001996516 fastq.gz 2.4 GB
EGAF00001996517 fastq.gz 2.4 GB
EGAF00001996518 fastq.gz 2.3 GB
EGAF00001996519 fastq.gz 2.3 GB
EGAF00001996520 fastq.gz 2.4 GB
EGAF00001996521 fastq.gz 2.4 GB
EGAF00001996522 fastq.gz 1.4 GB
EGAF00001996523 fastq.gz 1.4 GB
EGAF00001996524 fastq.gz 1.0 GB
EGAF00001996525 fastq.gz 1.1 GB
EGAF00001996526 fastq.gz 671.4 MB
EGAF00001996527 fastq.gz 679.9 MB
EGAF00001996528 fastq.gz 472.9 MB
EGAF00001996529 fastq.gz 470.6 MB
EGAF00001996530 fastq.gz 510.4 MB
EGAF00001996531 fastq.gz 509.4 MB
32 Files (58.3 GB)