|
| Status |
Public on Oct 25, 2020 |
| Title |
mpimg_L12976-1_CD1FLE9-5-cHiC |
| Sample type |
SRA |
| |
|
| Source name |
Forelimb
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Forelimb
genotype: Wild type
embryonic stage: E9.5
strain: c57bl6.J X 129S6.sv
|
| 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_L12976_L12977_L12978_CD1FLE9-5_Rep1_Rep2_Rep3_merged.hicup.MAPQ30.KR_10kb-cHiC.WashU.txt
mpimg_L12976_L12977_L12978_CD1FLE9-5_Rep1_Rep2_Rep3_merged.hicup.MAPQ30.Raw_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 |
|
| Relations |
| BioSample |
SAMN14733039 |
| SRA |
SRX8178502 |
