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Sample GSM759870 Query DataSets for GSM759870
Status Public on Mar 16, 2012
Title E10.5_hindlimb_ChIP_input_rep1
Sample type SRA
Source name embryonic hindlimb bud, ChIP input
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: hindlimb bud
developmental stage: gestational day E10.5
chip antibody: none
sequencing run type: Single-end 75
Treatment protocol Pregnant mothers were euthanized, and embryos were removed and placed in cold PBS. Forelimb and hindlimb buds were individually removed with forceps.
Growth protocol Normal mouse gestation to day 10.5.
Extracted molecule genomic DNA
Extraction protocol For each ChIP-Seq, limb bud tissue was crosslinked with 1% formaldehyde at room temperature and stored at -80°C. Chromatin was extracted and sheared by sonication. Soluble chromatin was combined with Protein G Dynabeads prebound with appropriate antibodies at 4C overnight. Beads were collected with magnet and washed 5x. Chromatin was eluted with TE+1%SDS at 65C for 10 minutes. Crosslinks were reversed at 65C overnight, and then chromatin was purified with the PCR cleanup kit (Qiagen).

Standard procedure included with the Illumina ChIP-Seq kit (IP-102-1001). For multiplexed samples, Illumina Multiplexing adapters and primers (PE-400-1001) were used instead of those provided with the ChIP-Seq kit. Multiplexed samples were paired-end sequenced with an insert size of 300 bp. Standard procedure included with the Illumina mRNA-seq kit (RS-100-0801).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Description Input
Data processing ChIP-Seq alignments: ChiP-Seq reads were aligned with bowtie (0.12.3) to the mouse genome (mm9) retaining only uniquely mapped reads (command: bowtie -m 1 -p 8 -B 1 --solexa1.3-quals ~/GENOME/mm9/dna/mm9_nh).

ChIP-Seq peak calling: ChIP peaks were identified by MACS (1.37) against input controls. Default parameters were used for CTCF ChIP-Seq (input control replicates 1 and 2)(command: macs -t ../../s_6_sequence.aligned -c ../../s_5_sequence.aligned --name=Mouse_CTCF_091310_FL_mfold10_p00001 --format=BOWTIE --tsize=74 --gsize=1860000000 --bw=150 -- pvalue=0.00001 --diag --mfold=10 --wig). Nomodel option was selected for H3K27me3 and H3K27ac ChIP seq (input control replicates 3 and 4 respectively)(command: macs -t ../082310/bowtie/s_5_sequence.aligned -c ../082210/bowtie/s_4_sequence.aligned --name=Mouse_h3k27me3_FL1_p00001 --nomodel --shiftsize=1 --format=BOWTIE --tsi ze=74 --gsize=1860000000 --bw=150 --pvalue=0.00001 --diag).
Submission date Jul 13, 2011
Last update date May 15, 2019
Contact name Justin Cotney
Organization name UConn Health
Department Genetics and Genome Sciences
Lab Cotney Lab
Street address 400 Farmington Ave.
City Farmington
State/province CT
ZIP/Postal code 06030-6403
Country USA
Platform ID GPL11002
Series (1)
GSE30641 Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb.
SRA SRX083269
BioSample SAMN00668308
Named Annotation

Supplementary file Size Download File type/resource 310.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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