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| Status |
Public on Jun 12, 2019 |
| Title |
T47D_HA_GATA3_TR2_aHA_siFOXA1_rep2 |
| Sample type |
SRA |
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| Source name |
T47D_HA_GATA3_TR2_aHA_siFOXA1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
cell type: Breast cancer cell line
chip antibody: aHA (05-904, Millipore)
plasmid: HA_GATA3_TR2 plasmid
sirna: siFOXA1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitations were performed as described previously, with adaptations (Schmidt et al., 2009). In short, cells were crosslinked in solution A (pH 7.4, 50mM Hepes, 100mM NaCl, 1mM EDTA, 0.5M EGTA) containing 2mM DSG for 35 minutes, then formaldehyde was added to a final concentration of 1% and incubated for another 10 minutes. After addition of Glycine to a final concentration of 125mM to quench the crosslinking reaction and washing with PBS, cells were collected. The Bioruptor Pico (Diagenode) was used for sonication. For ChIP, antibodies were used to detect the HA-tag (25mg, 05-904, Millipore) and GATA3 (10 mg, sc-268, Santa Cruz) with 100 ml Protein A magnetic beads (Thermo Scientific).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).
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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 |
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (v1.5) and MACS (v1.4) peak caller. Only peaks called by both algorithms were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: filtered.intersect files contain peaks called by both peak calling algorithms in bed format
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| Submission date |
Nov 23, 2018 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Lisette Cornelissen |
| E-mail(s) |
l.cornelissen@nki.nl
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| Organization name |
The Netherlands Cancer Institute
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| ZIP/Postal code |
1066 CX |
| Country |
Netherlands |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE122847 |
Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice [ChIP-seq] |
| GSE122849 |
Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice |
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| Relations |
| BioSample |
SAMN10471401 |
| SRA |
SRX5057630 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3486935_T47D_HA_GATA3_TR2_aHA_siFOXA1_rep2_filtered.intersect.bed.gz |
14.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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