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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jun 02, 2016 |
Title |
Fetal liver Knockout of alpha globin regulatory elements R1 and R2, biological replicate 2 [Capture C] |
Sample type |
SRA |
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Source name |
Erythroid cells
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Organism |
Mus musculus |
Characteristics |
knockout of enhancer-like component: regulatory elements R1 and R2 strain: F1 C57Bl6 / CBA tissue: Fetal Liver Culture genes analysed: Hba-a1&2, Hbb-b1&2, Slc25A37
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Extracted molecule |
genomic DNA |
Extraction protocol |
Fetal livers were dissected from E12.5 mouse embryos and the dissociated cell suspension was expanded for 5-7 days in Stempro (Invitrogen) supplemented with Epo (1U/ml), SCF (50ng/ml) and dexamethasone (1mM). Following expansion of the cultures, mature red cells were removed by negative selection for Ter119 using anti-Ter-119 magnetic beads (Miltenyi), to obtain a population of erythroid precursors. Cultures were then switched to medium containing high Epo (5U/ml) to induce differentiation to mature erythroid cells. After 18hrs differentiation, 3C libraries were prepared. The protocol used for generation of the 3C libraries was similar to previous methods with minor modifications. Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using either the Illumina MiSeq (150bp paired end reads) or HiSeq (100bp paired end reads). The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage). Oligonucleotide capture technology was then used to pull down the restricion fragments containing the promoters of the genes of interest and their interacting partners, which were subsequently idendified by high throughput sequencing. The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Description |
molecule: Next generation Capture-C product 3C library prepartion followed by double oligonucleotide capture HbaCombined_Enhancer_KO_30gH_Combined_PF_BF.gfc HbbCombined_Enhancer_KO_30gH_Combined_PF_BF.gfc Slc25A37_Enhancer_KO_30gH_Combined_PF_BF.gfc
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Data processing |
Library strategy: Capture-C Trim_galore (to remove sequencing adaptors) FLASH (to reconstruct paired end reads into single reads where possible) In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl) Alignment to the genome (Bowtie) maintaining strict read order Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl) Combining data from multiple replicates (custom scripts) Removal of ploidy regions and off target capture (custom scripts) Analysis in R to normalise between tracks using the total number of informative interactions Genome_build: mm9 Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
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Submission date |
Mar 01, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Jim Hughes |
E-mail(s) |
jim.hughes@imm.ox.ac.uk
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Phone |
1865222113
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Organization name |
University of Oxford
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Department |
MHU
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Lab |
Genome Biology Group
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Street address |
Weatherall Institute Of Molecular Me
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City |
oxford |
ZIP/Postal code |
OX3 9DS |
Country |
United Kingdom |
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Platform ID |
GPL16417 |
Series (2) |
GSE78803 |
Dissection of a super-enhancer in vivo (Capture-C) |
GSE78835 |
Genetic dissection of the α-globin super-enhancer |
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Relations |
BioSample |
SAMN04528765 |
SRA |
SRX1609510 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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