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| Status |
Public on Sep 10, 2014 |
| Title |
H19101_LCL |
| Sample type |
SRA |
| |
|
| Source name |
LCL
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| Organism |
Homo sapiens |
| Characteristics |
cell type (precursor used to generate ipscs): LCL
passage: n/a
gender: Male
|
| Treatment protocol |
n/a
|
| Growth protocol |
Standard iPSC and precursor cell line conditions as described in text
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen Rneasy
TruSeq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 25
|
| Data processing |
Mapping with TopHat2/Bowtie2
Removal of reads that do not map to highly orthologous regions between human and chimpanzee with featureCounts
Loess normalization on log2 CPM using voom
RPKM calculation
Genome_build: hg19
Supplementary_files_format_and_content: Processed data .txt file reports RPKMs
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| Submission date |
Sep 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Irene Gallego Romero |
| E-mail(s) |
ireneg@uchicago.edu
|
| Phone |
773 834 1984
|
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Gilad
|
| Street address |
920 E 58th St, CLSC 317
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE60996 |
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (RNA-Seq) |
| GSE61343 |
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics |
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| Relations |
| BioSample |
SAMN03015263 |
| SRA |
SRX690965 |
| 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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