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| Status |
Public on May 30, 2013 |
| Title |
delSXC9-Input |
| Sample type |
SRA |
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| Source name |
delSXC9 3hr dox
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| Organism |
Mus musculus |
| Characteristics |
cell line: delSXC9
cell type: embryonic stem cell
induction time: 3 hours
experiment type: Input
gender: male
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| Growth protocol |
Male ES cells were grown on plates coated with 0.2% gelatin in serum-free 2i/LIF media composed as follows: 1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy). Xist expression was induced by adding 2 micrograms per milliliter (ug/mL) doxycycline at a defined time before harvesting cells.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA Antisense Purification (RAP) was performed as described in Engreitz et al. 2013
NEBNext ChIP-Seq Library Prep Kit
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Input DNA (after preclear) for delSXC9 male embryonic stem cells induced with doxycycline
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| Data processing |
Library strategy: RAP-Seq
Align: BWA version 0.5.9 with default parameters
Filter: Remove reads with mapping qualities less than 30 or if flagged as PCR duplicates for both read pairs by Picard
Count: Count read-pairs that overlap a given window in the genome
Normalize: Divide read-pair count in a RAP experiment by the read-pair count in the input + 0.1
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files represent normalized enrichment ratios in windows across the genome. Windows deemed "unmappable" are omitted (see Engreitz et al. 2013). For the pSM33 timecourse, replicate Xist RAP experiments were combined to generate the final processed data. For pSM33 timecourse and female ES timecourse, counts in the input files were also combined across time points.
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| Submission date |
May 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jesse Engreitz |
| Organization name |
Broad Institute
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| Street address |
415 Main Street
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE46918 |
Xist exploits three-dimensional chromosome architecture to spread across the X-chromosome |
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| Relations |
| BioSample |
SAMN02144162 |
| SRA |
SRX277963 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not provided for this record |
| Raw data are available in SRA |
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