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Status |
Public on May 10, 2012 |
Title |
ChIP_Seq_p300_IMR90 |
Sample type |
SRA |
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Source name |
Lung fibroblast
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Organism |
Homo sapiens |
Characteristics |
strain: IMR90 antibody: p300 [Manufacturer: Santa Cruz, Catalog:SC-585XS, Lot#: E2209] cell type: Lung fibroblast
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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 HiSeq 2000 |
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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 |
May 15, 2019 |
Contact name |
Nisha Rajagopal |
E-mail(s) |
nirajago@ucsd.edu
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Phone |
8583738328
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Organization name |
UCSD
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Lab |
Bing Ren
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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 |
GPL11154 |
Series (1) |
GSE37858 |
A Random-Forest Based Algorithm for Prediction of Enhancers From Histone Modifications |
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Relations |
SRA |
SRX147007 |
BioSample |
SAMN00991811 |
Supplementary file |
Size |
Download |
File type/resource |
GSM929090_ChIP_Seq_p300_IMR90.bed.gz |
88.9 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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