Cornelissen 2019, ERα over-expression does not accelerate development of p53-deficient mammary tumors in mice.

Genome binding profiling by high throughput sequencing of exogenously introduced mouse and human ERα in an existing p53-deficiency driven breast cancer mouse model.

• Raw data was downloaded from: SRP187558
• Input file format: SRA
• Download date: 21-4-2020

From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	GSM3640241.sga	MMECs GEM|Input-HA||rep1	Input-HA	GSM3640241
2	GSM3640242.sga	MMECs GEM|Input-HA||rep2	Input-HA	GSM3640242
3	GSM3640243.sga	MMECs GEM|ESR1-HA||rep1	ESR1-HA	GSM3640243
4	GSM3640244.sga	MMECs GEM|ESR1-HA||rep2	ESR1-HA	GSM3640244
5	GSM3640245.sga	MMECs GEM|Esr1-HA||rep1	Esr1-HA	GSM3640245
6	GSM3640246.sga	MMECs GEM|Esr1-HA||rep2	Esr1-HA	GSM3640246

Notes on samples nomenclature:

MMECs GEM stands for genetically engineered mouse mammary epithelial cells.

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v1.2.2. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.5).

• Cornelissen LM, Henneman L, Drenth AP, Schut E, de Bruijn R, Klarenbeek S, Zwart W, Jonkers J
  Exogenous ERα Expression in the Mammary Epithelium Decreases Over Time and Does Not Contribute to p53-Deficient Mammary Tumor Formation in Mice. J Mammary Gland Biol Neoplasia. 2019 Dec;24(4):305-321. doi: 10.1007/s10911-019-09437-z. Epub 2019 Nov 15. 31729597
• GEO series GSE127859: ERα over-expression does not accelerate development of p53-deficient mammary tumors in mice [ChIP-Seq]