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| Status |
Public on Jul 14, 2015 |
| Title |
IP_293T_B4N_N |
| Sample type |
SRA |
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| Source name |
293T
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| Organism |
Homo sapiens |
| Characteristics |
cell type: 293Trex (cells originating from embryonic kidney)
cell line: 293T_B4N_N
pulldown with biotap_tag: N- BioTAP-BRD4-NUT
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| Treatment protocol |
797TRex and 293TRex cells, which contain a single genomic FRT recombination site, were maintained as above with Blasticidin (Invitrogen). TC-797 and 293-TRex /N- and C- BioTAP-BRD4-NUT lines were generated by recombination with the plasmids pcDNA5 FRT/TO/N- or C-BioTAP BRD4NUT using the Flp-In technology manufacturer’s instructions (Invitrogen). The resulting cell lines were maintained in medium supplemented with Blasticidin (Invitrogen) and Hygromycin (Sigma).
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| Growth protocol |
293Trex cells and TC-797 (Toretsky et al. 2003) were maintained in Dulbecco Modified Eagle medium (DMEM) (Invitrogen) supplemented with 10% (v/v) Fetal Bovine Serum (FBS, S10350, Atlanta)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
1.5 × 109 cells grown as monolayer cultures in 150mm dishes (100 plates total) were used for BioTAP-XL purification. Tetracycline was added (1 μg/mL) to 60-70 % confluent culture to induce transcription of the N- or C-BioTAP tagged BRD4-NUT cDNA clones for 16h. The main steps of BioTAP-XL procedure: harvesting cells, formaldehyde cross-linking, chromatin preparation, affinity purification, input and IP DNA recovery, and ChIP-seq library preparation, were performed as described (Alekseyenko et al. 2014a; Alekseyenko et al. 2015)
ChIP-seq library preparation, were performed as described (Alekseyenko et al. 2014a; Alekseyenko et al. 2015)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were aligned to the human reference genome (GRCh38 assembly) using Bowtie (version 0.12.5), retaining only uniquely mapped reads.
Smoothed enrichment profiles were generated using the SPP package (Kharchenko et al. 2008), using smoothing bandwidth of 5kb.
tdf files were generated by converting wig files using igvtools
Genome_build: GRCh38
Supplementary_files_format_and_content: TDF files (for IGV browser) containing conservative estimates of smoothed enrichment
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| Submission date |
Jul 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Kharchenko |
| Organization name |
Harvard Medical School
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| Department |
DBMI
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| Lab |
Kharchenko
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| Street address |
10 Shattuck St.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE70868 |
The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains |
| GSE70869 |
Chip-seq BRD4NUT-BioTAP mapping in 293Trex and 797 cells |
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| Relations |
| BioSample |
SAMN03857499 |
| SRA |
SRX1094460 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1820921_IP_B4N_N_293T_VS_Input_B4N_N_293T.smoothed.enrich.tdf |
256.3 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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