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| Status |
Public on Sep 21, 2013 |
| Title |
Hela Input 20F8A9 12333 |
| Sample type |
SRA |
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| Source name |
Hela_Input_20F8A9
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
chip antibody: none
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| Growth protocol |
HeLaS3 cells were cultured in Dulbeco's modified Eagle's medium (DMEM, Invitrogen #11955) containing 10% bovine serum (Invitrogen #16170), penicillin and streptomycin, and L-glutamine (2mM). Cells were fed 24 hours before harvest for ChIP-seq, which was performed at 80-90% confluency.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed for 10min at RT in 1% formaldehyde, harvested using a cell scraper, washed once in ice-cold PBS, and resuspended in RIPA buffer with protease inhibitor. The sample was then sonicated using an 3.2mm microtip (QSonica Sonicator 4000) at 30s on 30s off intervals and 40% amplitude for 180min while in a -30C 3:1 isopropanol and water bath containing dry ice. Subsequent steps were performed as per the standard protocol. DNA was size-selected during library building to an average fragment size of 200bp. Libraries were sequenced using Illumina HiSeq 2000.
Libraries were generated following Illumina's DNA Sample Prep Kit protocol
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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: Casava1.8
read alignment: Bowtie 0.12.7, separate alignments against the nuclear and mitochondrial genomes
bedgraph track generation: custom-written python script
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph of read coverage, normalized to RPM (Read Per Million); separate tracks for the nuclear and mitochondrial genomes
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| Submission date |
Jun 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Georgi Kolev Marinov |
| Organization name |
STANFORD UNIVERSITY
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| Department |
Genetics
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| Street address |
279 Campus Drive West, Beckman Center, B-257A/259
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| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5101 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
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| Relations |
| BioSample |
SAMN02210002 |
| SRA |
SRX312238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1171655_Hela-Input-PrepK-12333.36mers.v0.chrM.wig.bedGraph.gz |
132.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM1171655_Hela-Input-PrepK-12333.36mers.v0.unique-nochrM.wig.bedGraph.gz |
132.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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