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Sample GSM4110042 Query DataSets for GSM4110042
Status Public on Apr 25, 2020
Title FB_E12_5_WT_Hoxd13VP
Sample type SRA
 
Source name forebrain
Organism Mus musculus
Characteristics genotype: wildtype
developmental stage: E12.5
strain: CBA / C57BL/6 mix
Extracted molecule genomic DNA
Extraction protocol Circular chromosome conformation capture (4C-seq) was performed as described in (Noordermeer et al., 2011). Briefly, tissues (20-40 GT or 40 cloaca) were isolated in PBS supplemented with 10% Fetal Calf Serum and dissociated to single cell by collagenase treatment. Samples were fixed in 2% formaldehyde, lysed, and stored at −80°C. Samples were primarily digested with NlaIII (NEB, R0125L) followed by ligation under diluted conditions. After decrosslinking and DNA purification DpnII (NEB, R0543M) was used for the second restriction. All ligation steps were performed using highly concentrated T4 DNA ligase (Promega, M1794). For each viewpoint approximately 1μg of DNA was amplified by using 12 individual PCR reactions.
Libraries were constructed with inverse primers for different viewpoints (see Table 5) containing Illumina Solexa adapter sequences and sequenced on an Illumina HiSeq 2500 sequencer, as single-end reads (read length 100 base pairs or 80 base pairs). In some samples 4-bp barcodes were added between the adapter and each specific viewpoint to allow sample multiplexing.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Library strategy: 4C-seq
4C-seq reads were demultiplexed, mapped on GRCm38/mm10 mouse assembly, and analyzed using the 4C-seq pipeline of the Bioinformatics and Biostatistics Core Facility (BBCF) HTSstation (http://htsstation.epfl.ch) (David et al., 2014) or using a local version of it using the facilities of the Scientific IT and Application Support Center of EPFL. Profiles were normalized to a 5Mb region surrounding the HoxD cluster and smoothened using a window size of 11 fragments
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
 
Submission date Oct 07, 2019
Last update date Apr 26, 2020
Contact name Ana Rita Amandio Lhopitallier
E-mail(s) rita.lhopitallier@epfl.ch
Organization name EPFL
Department SV-ISREC-EPFL
Lab Laboratory of Developmental Genomics
Street address SV2842, Station 19
City Lausanne
ZIP/Postal code CH-1015
Country Switzerland
 
Platform ID GPL17021
Series (2)
GSE138507 A complex regulatory landscape involved in the development of external genitals [4C-seq]
GSE138514 A complex regulatory landscape involved in the development of external genitals
Relations
BioSample SAMN12983218
SRA SRX6958274

Supplementary file Size Download File type/resource
GSM4110042_FB_E12_5_WT_Hoxd13VP.bedGraph.gz 2.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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