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| Status |
Public on May 10, 2012 |
| Title |
ChIP_Seq_p300_H1 |
| Sample type |
SRA |
| |
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| Source name |
Embryonic Stem Cells
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| Organism |
Homo sapiens |
| Characteristics |
strain: H1
antibody: p300 [Manufacturer: Santa Cruz, Catalog:SC-585XS, Lot#: E2209]
cell type: Embryonic Stem Cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
base-calling using Illumina software with output as Fastq files
Sample 1 and 2:alignment and mapping with Bowtie with seed length 32bp,maximum matches 1 and maximum mismatches 2.Output was bowtie_output or BAM file.; Sample 3: alignment and mapping with Illumnia's ELAND software using seed length of 25bp and maximum number of mismatches 2
Bed files were created using custom perl scripts. Read length of 36bp was used and only reads that mapped uniquely were used. Polyclonal reads were reduced to one instance.
Genome_build: hg18
Supplementary_files_format_and_content: bed files
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| Submission date |
May 08, 2012 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Nisha Rajagopal |
| E-mail(s) |
nirajago@ucsd.edu
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| Phone |
8583738328
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| Organization name |
UCSD
|
| Lab |
Bing Ren
|
| Street address |
9106 REGENTS RD APT F
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| City |
LA JOLLA |
| State/province |
CA |
| ZIP/Postal code |
92037-1445 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (1) |
| GSE37858 |
A Random-Forest Based Algorithm for Prediction of Enhancers From Histone Modifications |
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| Relations |
| BioSample |
SAMN02197534 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM929092_ChIP_Seq_p300_H1.bed.gz |
81.5 Mb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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