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| Status |
Public on Apr 04, 2016 |
| Title |
Level 2 promoters in human KP cells |
| Sample type |
SRA |
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| Source name |
KP
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| Organism |
Homo sapiens |
| Characteristics |
cell type: KP
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| Treatment protocol |
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).
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| Extracted molecule |
total RNA |
| Extraction protocol |
CAGE-seq was performed by DNAFORM Inc. at RIKEN Omics Science Center. The samples were prepared according to the OP-SOLEXA-96CAGE-v.3.0.
The sequencing run and the base call analysis were performed according to the manufacturer's protocol Illumina Sequencing Kit v4.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
CAGE |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
After the sequencing, sequence raw data were generated with processing by GenomeAnalyzer Iix. For CAGE tags mapping to multiple genome locations, a weighting strategy based on the number of CAGE tags within a 200 bp neighbourhood around each candidate mapping location was applied. (Faulkner GJ, et al 2008).
Level-1 promoters (TSSs) were created by summing the weighted number of CAGE tags at each genome position. We required at least one CAGE tag in at least one experimental condition; other mapping positions were discarded. The level-1 promoters were clustered into Level-2 promoters (CAGE-promoters) if they were within 20 bp of each other on the same chromosomal strand. We required that the expression of each level-2 promoter was at least 10 tpm in at least one experimental condition; other promoters were dropped.
Genome_build: Hg19
Supplementary_files_format_and_content: The bed file contains the genomic regions of the level-2 promoters and the TPM levels.
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| Submission date |
Dec 17, 2014 |
| 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 |
GPL10999 |
| Series (2) |
| GSE64297 |
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (CAGE) |
| GSE64328 |
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation |
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| Relations |
| BioSample |
SAMN03268515 |
| SRA |
SRX816540 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1568243_KP_CAGE.bed.gz |
183.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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