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| Status |
Public on Apr 21, 2016 |
| Title |
SSC_input_3 |
| Sample type |
SRA |
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| Source name |
Spermatogonial stem and progenitor cell (SSC)
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| Organism |
Mus musculus |
| Characteristics |
strain: 129mix
chip antibody: none
cell type: Spermatogonial stem and progenitor cell (SSC)
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| Growth protocol |
Mouse SSCs were cultured on MEFs in SSC medium containing StemPro-34 (Invitrogen) and supplements as follows: D(+) glucose, 6 mg/ml; BSA, 0.50%; insulin, 25 μg/ml (Sigma-Aldrich); MEM nonessential amino acids, 1× (Gibco); MEM vitamin solution, 1× (Gibco); penicillin (100 U/ml)/streptomycin (100 μg/ml)/amphotericin (0.2 μg/ml) (Media-tech); fetal bovine serum, 1%; L-glutamine, 2 mM (Media-tech); Bovine holo-transferrin, 100 μg/ml (Sigma-Aldrich); β-estradiol, 30 ng/ml (Calbiochem); progesterone, 60 ng/ml (Calbiochem); putrescine, 60 μM (Research Organics); sodium selenite, 30 nM (Sigma-Aldrich); pyruvic acid, 30 μg/ml (Sigma-Aldrich); d(L)-lactic acid, 1 μg/ml (Baker); β-mercaptoethanol, 50 μM (Gibco); ascorbic acid, 100 μM (EMD); D-biotin, 10 μg/ml (Calbiochem); human GDNF, 10 ng/ml (R&D Systems); human bFGF, 10 ng/ml (Cell Signaling); mouse EGF, 20 ng/ml (R&D Systems). To remove residual feeder cells in the collection, cells were plated in gelatin-coated plates in fresh SSC medium for 2 hours. All the floating cells were then gently collected, washed once in PBS, and subjected to experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was performed with 1x10^7 cells per experiment. The cells were collected and cross-linked for 15min in 1% paraformaldehyde, washed and lysed. Chromatin was sheared using a Bioruptor to create fragments of approximately 150 base pairs, incubated with about 2–5 μg antibody bound to 75 μl Dynabeads M-280 (Invitrogen) and rotated overnight at 4 °C, then washed and eluted. The eluted chromatin was reverse-cross-linked and column purified.
ChIP samples were prepared for sequencing using Illumina TruSeq DNA Sample Preparation Kit according to the standard preparation protocol.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using BWA (version 0.5.9) with default parameters
Duplicates were removed using Picard (version 1.69).
The software ChIPseeqer 2.0 was applied to the ChIP-seq data with sequencing data from input DNA as control to identify genomic enrichment (peak) of specific histone modifications (FDR<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: bed files include all unique reads that mapped to a single best-matching location.
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| Submission date |
Feb 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ying Liu |
| E-mail(s) |
yil2004@med.cornell.edu
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| Organization name |
Weill Cornell Medical College
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| Department |
Medicine
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| Street address |
1300 York Ave
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL15103 |
| Series (1) |
| GSE78129 |
Epigenetic Profiles Signify Cell Fate Plasticity in Unipotent Spermatogonial Stem and Progenitor Cells (ChIP-Seq) |
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| Relations |
| BioSample |
SAMN04505027 |
| SRA |
SRX1594770 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2067714_SSC_input_3.bed.gz |
31.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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