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| Status |
Public on Aug 13, 2014 |
| Title |
E12.5_histone_input |
| Sample type |
SRA |
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| Source name |
Heart
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| Organism |
Mus musculus |
| Characteristics |
tissue: primary heart tissues
age: E12.5
chip antibody: none (input)
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| Treatment protocol |
Gata4fbio, Rosa26BirA, cTNTcre, and Gata4flox alleles were described previously(He, et al. G&D 2012; Circ Res 2012).
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| Growth protocol |
All animal procedures were approved by the Institutional Animal Care and Use Committee of Boston Children’s Hospital.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
RNA-seq and ChIP-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit.
2 µg of pooled RNA were used for two rounds of poly(A) mRNA purification by Dynabeads Oligo(dT)25 (Invitrogen). RNA was reverse transcribed by SuperScript III (Invitrogen) and random hexamer primers. After RNaseH treatment and PolI catalyzed 2nd-strand cDNA synthesis, DNA end repair was achieved by End-it kit (Epicnetre). DNA was then A-tailed with Exo- Klenow (NEB), and adaptors were ligated using Quick T4 DNA Ligase (NEB).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
E12.5
Total_DNA
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| Data processing |
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the UCSC mm9 genome assembly using tophat version 1.4, reads were count using htseq-count version 0.5.3
ChIP-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.5.9, peaks were called using MACS 1.4
Genome_build: UCSC mm9
Supplementary_files_format_and_content: bigwig files report ChIP-seq peaks, txt files report RNA-seq counts.
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| Submission date |
Nov 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Fei Gu |
| E-mail(s) |
alickgf@hotmail.com
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| Organization name |
Childrens hospital boston, Harvard Medical School
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| Department |
Cardiology
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| Lab |
William Pu
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| Street address |
320 Longwood Ave.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE52123 |
Reinstatement of developmental stage-specific GATA4 enhancers controls the gene expression program in heart disease |
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| Relations |
| BioSample |
SAMN02397345 |
| SRA |
SRX373604 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1260034_E12.5_histone_input.bw |
796.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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