|
| Status |
Public on May 30, 2013 |
| Title |
Female-6hr-Xist |
| Sample type |
SRA |
| |
|
| Source name |
F1 2-1 6hr retinoic acid
|
| Organism |
Mus musculus |
| Characteristics |
cell line: F1 2-1
cell type: embryonic stem cell
induction time: 6 hours
experiment type: Xist RAP
gender: female
|
| Growth protocol |
Female ES cells were cultured in medium containing Knockout DMEM (Life Technologies) supplemented with 15% fetal calf serum (GlobalStem), 1X NEAA (Life Technologies), 2 mM L-glutamine (Life Technologies), 0.1 mM beta-mercaptoethanol (Sigma), with or without 1000U/mL LIF (GlobalStem) on a mitotically inactivated male MEF feeder layer. At the start of the experiment, the ES cells were passaged using 0.05% trypsin and pre-plated for 45 minutes in ES medium onto plates treated with 0.3% gelatin to deplete MEFs from the culture. ES cells were then collected and seeded onto plates coated with 0.3% gelatin at a density of 15K cells/cm2 and plated in in ES medium + 1000U/mL LIF. Cells were all cultured for 48 hours and all-trans retinoic acid (RA) (Sigma) was added at different time points. At each time point, medium was removed from the culture and replaced with ES medium lacking LIF and supplemented with freshly diluted 1uM RA.
|
| 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
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RAP-Seq using probes targeting Xist on female embryonic stem cells differentiated with retinoic acid
|
| 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.
|
| |
|
| Submission date |
May 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jesse Engreitz |
| Organization name |
Broad Institute
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE46918 |
Xist exploits three-dimensional chromosome architecture to spread across the X-chromosome |
|
| Relations |
| BioSample |
SAMN02144176 |
| SRA |
SRX277977 |
| Named Annotation |
GSM1141199_Female-6hr-Xist_vs_Input.W10000_O7500.bigWig |
