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| Status |
Public on Feb 03, 2015 |
| Title |
cFA07_3_KDRC34_d6 |
| Sample type |
SRA |
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| Source name |
patient-specific iPSCs
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hemoangiogenic progenitors
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| Treatment protocol |
Hemoangiogenic progenitor cells were srtained with CD34 and KDR antibodies, and sorted by Aria-Ⅱ.
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| Growth protocol |
PSCs were differentiated into hemoangiogenic progenitor cells under serum- and feeder-free monolayer differentiation system.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from sorted hemoangiogenic progenitors using RNAeasy (Qiagen) kit.
We synthesized double-stranded cDNA from single stranded cDNA using PrimeScript Double Strand cDNA Synthesis Kit (TaKaRa). The double-stranded cDNA was then sheared in an AFA microtube using Covaris E210 (Covaris Inc., Woburn, MA, USA) withthe following settings: Intensity 5, Duty Cycle 10%, Cycles/burst 200, Treatment time 120s. Illumina libraries were prepared using 0.43 - 2.62ng of sheared cDNAs by Low Input Library Prep Kit (Clontech Laboratories Inc., Palo Alto, CA, USA) with 8 cycles PCR amplifications.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Data were filtered using Illumina's Quality Filtering and 101th bases in reads were not used.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.8b with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calcurated using RPKMforGenes, downloaded on 19th, October 2012..
Genome_build: hg19
Supplementary_files_format_and_content: Text files which contain RPKM were calcurated using RPKMforGenes, downloaded on 19th, October 2012.
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| Submission date |
Feb 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Megumu Saito |
| E-mail(s) |
msaito@cira.kyoto-u.ac.jp
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| Organization name |
Kyoto University
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| Street address |
53, Shogoin-Kawahara
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| City |
Kyoto |
| ZIP/Postal code |
6068507 |
| Country |
Japan |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE65507 |
Pluripotent cell models of Fanconi anemia identify the early pathological defect in human hemoangiogenic progenitors |
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| Relations |
| BioSample |
SAMN03324053 |
| SRA |
SRX863071 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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