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| Status |
Public on Apr 04, 2016 |
| Title |
DK Input DNA |
| Sample type |
SRA |
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| Source name |
DK
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Differentiated Keratinocytes
chip antibody: none
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| Growth protocol |
KP cells were obtained from foreskin biopsies of healthy neonatal donors and expanded by cultivation onto lethally irradiated 3T3-J2 cells in growth FAD medium, a DMEM and Ham’s F12 media mixture (2:1) containing FCS (10%), penicillin-streptomycin (1%), glutamine (2%), insulin(5ug/ml), adenine (24.3ug/ml), hydrocortisone (0.4ug/ml), cholera toxin (50ug/ml), triiodotyronine (2nM). DKs were cultivated in EpiLife serum-free medium (Invitrogen) containing EpiLife defined growth supplements (HKGS, Invitrogen), penicillin-streptomycin (1%) and glutamine (2%).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin preparation and processing was performed starting from pellets of 10e7 KP and DK cells and following the truChIP Chromatin Shering Kit standard protocol (PN520076, Covaris Inc.).
Libraries were prepared according to Illumina's instructions accompanying the standard protocol of Illumina ChIP-seq DNA sample preparation kit (IP-102-1001, Illumina Inc.).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
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| Data processing |
We mapped raw reads against the human reference genome (build hg19) using Bowtie allowing up to 2 or 3 mismatches
Peaks were obtained using MACS2 using default parameters
Genome_build: hg19
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| Submission date |
Feb 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Luca Petiti |
| E-mail(s) |
luca.petiti@itb.cnr.it
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| Organization name |
ITB-CNR
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| Street address |
Via Fratelli Cervi, 93
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| City |
Segrate |
| State/province |
Milan |
| ZIP/Postal code |
20090 |
| Country |
Italy |
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| Platform ID |
GPL15520 |
| Series (2) |
| GSE64298 |
Transcriptional Regulationand Chromatin Dynamics in Human Epithelial Cell Differentiation (ChIP-seq) |
| GSE64328 |
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation |
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| Relations |
| BioSample |
SAMN04519520 |
| SRA |
SRX1603679 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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