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| Status |
Public on Jul 12, 2017 |
| Title |
DFL_E12_WT_CTCF |
| Sample type |
SRA |
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| Source name |
Forelimb
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
age: E12.5
tissues: Distal forelimb
genotype: wild type
antibody: CTCF (Active motif REF# 61311)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Micro-dissected distal segments of E12.5 limbs from wild type CD1 mice, were used for ChIP-seq. Samples were fixed in 1% formaldehyde/PBS for 10 minutes at room temperature, washed three times with cold PBS containing protease inhibitor and stored at -80°C. One hundred milligrams of tissue were used. Nuclei were extracted by incubating them in a cell lysis buffer provided in the ChIP IT high sensitivity kit (Active motif) during at least 10 minutes and with the aid of A Dounce homogenizer type B (Active motif). The isolated nuclei were pelleted and lysed in sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH=8.0 and protease inhibitor) for 10 min on ice, and fragmented to a range of 200-500 bp using a Vibracell tip sonicator. DNA concentration was estimated using the Qubit ds DNA HS assay kit following manufacturer instruction and 25 ugr of chromatin were diluted ten times in ChIP dilution buffer (20mM HEPES, 150mM NaCl, 0.1% NP40) and incubated overnight at 4C with 4mgr of anti-CTCF antibody (Active motif) on a rotating platform. The next day chromatin-antibody complexes were incubated with protein A/G agarose beads during 3h at 4C and successively washed following manufacturer instructions. Finally they were eluted and purified by phenol:chlorophorm extraction and precipitation. A total of 10ngr of immunoprecipitated DNA were sequenced with a 50bp single-end Illumina HiSeq flow cell.
For ChIP-seq, 10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Distal forelimb mouse E12.5 WT CTCF ChIPseq
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| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed ChIP-seq reads were mapped against the mouse GRC38/mm10 genome assembly using the BBCF HTSstation (http://htsstation.epfl.ch and (David et al., 2014)) platform.
Genome_build: GCR38/mm10
Supplementary_files_format_and_content: Bigwig files of the ChiP seq mapped reads
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| Submission date |
Mar 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Pierre J Fabre |
| E-mail(s) |
fabre.pierre@gmail.com
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| Organization name |
EPFL
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| Department |
ISREC
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| Lab |
Laboratory of Developmental Genomics
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| Street address |
Station 19
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| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE96558 |
ChIP-seq analysis of CTCF in distal limbs at mouse E12.5 using anti-CTCF |
| GSE98233 |
Large-scale genomic reorganizations of topological domains (TADs) at the HoxD locus |
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| Relations |
| BioSample |
SAMN06564778 |
| SRA |
SRX2636937 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2535578_DFL_CTCF_e12.bw |
537.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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