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| Status |
Public on May 29, 2018 |
| Title |
H3K4me3_ChIPseq_Isolate_Rep2 |
| Sample type |
SRA |
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| Source name |
auditory forebrain_H3K4me3_ChIPseq
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| Organism |
Taeniopygia guttata |
| Characteristics |
age: Posthatch day 67
Sex: male
experience: Isolate
tissue: brain; auditory forebrain
chip antibody: H3K4me3 (Active Motif, #39159)
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| Growth protocol |
Tutored and Isolate P67 males were raised with either 1 adult male + 1 adult female (Tutored) or 2 adult females (Isolate) from P21 onward
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Aduitory forebrain was rapidly dissected, and frozen. Upon thawing tissue was fixed immediately1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on HiSeq 2500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Replciate 2
AB1_Slondon_IsoNew_H3K4me3_A001_r1
Isolate__H3K4me3_Rep2
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| Data processing |
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (50 nt reads, single end) were aligned to the taeGut2 using the BWA algorithm (v0.6.1, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7. --- or e.g.: Peak calling was done with the SICER script (SICER v1.1; FDR 1E-10, gap=600).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: taeGut2
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = standard BED file containing MACS peaks
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| Submission date |
Jan 29, 2018 |
| Last update date |
May 29, 2018 |
| Contact name |
Sarah E London |
| E-mail(s) |
london@uchicago.edu
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| Organization name |
University of Chicago
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| Street address |
940 E 57th Street
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL22780 |
| Series (1) |
| GSE91399 |
Epigenetic signature of extended critical period learning |
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| Relations |
| BioSample |
SAMN08434934 |
| SRA |
SRX3630062 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2970926_01_ABSlondon_IsoNew_H3K4me3_A001.mID.nudup.sorted.markdup_uniqnorm_hits-W200-G200-FDR1E-5-island.bed.gz |
166.0 Kb |
(ftp)(http) |
BED |
| GSM2970926_01_ABSlondon_IsoNew_H3K4me3_A001.mID.nudup.sorted.markdup_uniqnorm_signal.bw |
72.0 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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