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Sample GSM4498654 Query DataSets for GSM4498654
Status Public on Oct 25, 2020
Title mpimg_L19077-1_E9-5-FB-Rep2-cHiC
Sample type SRA
Source name Forebrain
Organism Mus musculus
Characteristics tissue: Forebrain
genotype: Wild type
embryonic stage: E9.5
strain: c57bl6.J X
Treatment protocol Limbs, forebrains, and midhindbrains from E9.5 or E10.5 mouse embryos were dissected in PBS, a single cell suspension was made using Trypsin, samples were fixed in 2% PFA, snap frozen, and stored at -80 °C.
Extracted molecule genomic DNA
Extraction protocol The capture HiC protocol was performed as decribed in (Formation of new chromatin domains determines pathogenecity of genomic duplications. Franke et al., Nature 2016).
Snap frozen samples were first digested using DpnII, religated using the T4 DNA ligase (Thermo Fisher Scientific). The chimeric chromatin products were then decrosslinked overnight. RNase A treated chromatin was then precipiated.The precipiated chromatin was sheared using a Covaris sonicator (duty cycle: 10%; intensity: 5; cycles per burst: 200; time: 6 cycles of 60 s each; set mode: frequency sweeping; temperature: 4–7 °C). Adaptors were added to the sheared DNA and amplified according to the manufacturer’s instructions for Illumina sequencing (Agilent). The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing following the manufacturer’s instructions (Agilent).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Description mpimg_L19076_L19077_L19078_E9-5-FB-Rep1_Rep2_Rep3_merged.hicup.MAPQ30.KR_10kb-cHiC.WashU.txt
Data processing Library strategy: capture HiC
Raw sequencing reads were processed with the HiCUP pipeline v0.6.1 (no size selection, Nofill: 1, Format: Sanger) using Bowtie2 v2.3.4.1 for mapping short reads. Replicates were then merged by combining their bam files.
Juicer tools v1.7.6 was used to generate binned contact maps and to normalize maps by Knights and Ruiz (KR) matrix balancing.
As an additional filtering step, read-pairs with genomic distances ≤ 10 kb were removed. Afterwards, cHi-C maps were generated with the Juicer tools ‘pre’ command using a custom chrom.sizes file containing only the length of the genomic region of interest (4.75 Mb) and requesting a MAPQ≥30.
Genome_build: Mm9
Submission date Apr 26, 2020
Last update date Oct 25, 2020
Contact name Lila Allou
Organization name Max Planck Institute For Molecular Genetics
Department FG Development and Disease
Lab FG Mundlos
Street address 63-73 Ihnestrasse
City Berlin
ZIP/Postal code 14195
Country Germany
Platform ID GPL17021
Series (2)
GSE137333 Loss of Maenli lncRNA expression causes engrailed-1 dependent congenital limb malformations [Capture Hi-C]
GSE137335 Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator
BioSample SAMN14733035
SRA SRX8178506

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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