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Sample GSM2251511 Query DataSets for GSM2251511
Status Public on Dec 06, 2016
Title RAD21-HL-E115-Wt-Mm-Rep2-L8226-1
Sample type SRA
Source name Embryonic Limb Bud
Organism Mus musculus
Characteristics tissue: hindlimb
developmental stages: E11.5
strain: CD1
chip antibody: RAD21 (Abcam: ab992)
Treatment protocol For chromatin modifications, chromatin was prepared from the different tissues with a 1% FA crosslinking for 15 minutes and resuspended in buffer 3 for sonication (Lee et al.,). For CTCF and RAD21 ChIP-seq we prepared chromatin as follow: tissues were disrupted in 0.1% collagenase at 37°C and homogenized using a needle. Cell were then centrifuged and resuspended in (10%FCS, 0.2%Cs, 1% L-Glu, 0.5% Pen-Strep in DMEM:HAM’s F-12 1:1)) and fixed in 1% FA for 10’ on ice. Cell were then lysed in buffer 1 and 2 and resuspended in buffer 3 for sonication (Lee et al. 2006).
Growth protocol Limb bud and midbrain were micro-dissected from mouse embryos
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
We sheared chromatin using Bioruptor until reaching a fragment size of 200-500bp. 10-15μg of chromatin was then used for each replicate chromatin modification ChIP and 30μg for CTCF and RAD21 ChIP. ChIP for H3K4me1 (Abcam: 8898), H3K4me3 (Milipore: 07-473), H3K27Ac (Diagenode: C1540174), H3K27me3 (Milipore: 07-449), CTCF (Active motif: 613111) and RAD21 (Abcam: ab992) was then performed as in Lee et al., 2006. Libraries were prepared using the Nextera adaptors and sequenced.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Description The file for this sample is available on GSM2251510
Data processing Single-end reads from ChIP-seq experiments were mapped with Bowtie-2.2.6 to reference genome mm9. Mapped reads were filtered for mapping quality ≥10, and duplicates were removed.
Reads were extended to a length of 300bp and a scaled (one million / total of unique reads) coverage was computed using genomeCoverageBed from bedtools. We then produced the bigwig files using bedGraphToBigWig tool from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
Submission date Jul 25, 2016
Last update date May 15, 2019
Contact name Guillaume Andrey
Phone +41223795703
Organization name University of Geneva
Department Department of Genetic Medicine and Development
Street address Rue Michel-Servet 1
City Geneva
ZIP/Postal code 1211
Country Switzerland
Platform ID GPL17021
Series (2)
GSE84793 Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding [ChIP-seq]
GSE84795 Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
BioSample SAMN05438954
SRA SRX1975356

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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