|
| Status |
Public on Feb 14, 2014 |
| Title |
RNA Pol II ChIP-seq Coc Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
NAc dissection from 3-5 animals
|
| Organism |
Mus musculus |
| Characteristics |
tissue: nucleus accumbens
strain: C57BL/6
chip antibody: RNA Pol II
treatment: Repeated cocaine I.P. injection for 1w at 20mg/kg
chip antibody vendor/catalog: Abcam Cat#ab5408
passages: N/A
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslink with 1% formaldehyde for 10 min and pool 20 NAc for one replicate. Homogenize and sonicate by using bioruptor.
Antibodies were all ChIP grade from Abcam. Around ten nanograms of input DNA or pull-down DNA was used for sequencing library prep following the instructions of Illumina’s ChIP-seq sample prep kit (cat#IP-102-1001). In brief, DNA fragment overhangs were converted into phosphorylated blunt ends, using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. An “A” base was then added to the DNA fragments to enable ligation to the adapters, which have a single “T” overhang. The constructed library was then run on a 2% agarose gel and size selected between 175-300 bp. Lastly, gel-extracted DNA was further enriched by PCR and run on a bioanalyzer to validate size distribution and concentration.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
diff.pol2.res.annotated
|
| Data processing |
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Illumina ELAND with default configurations
Uniquely aligned reads were kept and further filtered with PCR redundancy (See Supplemental for details).
Differential sites were found by diffReps (http://code.google.com/p/diffreps/) with window size 200bp and step size 20bp. An FDR<10% was used as cutoff.
genome build: mm9
processed data files format and content: diffReps output is a tab-delimited text file which contains information for each differential site. Each differential site is also annotated by its proximity to genes or heterochromatic regions.
processed data files format and content: BED files contain six columns that represent uniquely aligned, PCR redundancy removed alignments. Columns 4 and 5 are not used.
processed data files format and content: bigWig files are binary representation of wiggle files (http://genome.ucsc.edu/goldenPath/help/bigWig.html). They are converted from the BED files above using the BedTools (https://code.google.com/p/bedtools/).
|
| |
|
| Submission date |
Dec 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Shen |
| E-mail(s) |
li.shen@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Lab |
Shen
|
| Street address |
1425 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE42810 |
Chronic cocaine-regulated epigenome in mouse [ChIP-Seq] |
| GSE42811 |
Chronic cocaine-regulated epigenome in mouse |
|
| Relations |
| SRA |
SRX209215 |
| BioSample |
SAMN01828059 |
