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| Status |
Public on Jul 01, 2017 |
| Title |
UnrelatedSet1_GM12878 |
| Sample type |
SRA |
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| Source name |
cultured B-cells
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| Organism |
Homo sapiens |
| Characteristics |
sample: GM12878
family: 1463
relation: mother
protocol: non-directional
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| Growth protocol |
Cultured B-cell lines were obtained from Coriell (Camden, NJ, USA). The B-cells were grown to a density of 5x105 cells/mL in RPMI 1640 supplemented with 15% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/L L-glutamine.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq libraries were prepared following Illumina's recommendations. Briefly, cells were harvested 24 hours after addition of fresh medium, and total RNA was extracted using the RNeasy Mini kit with DNase treatment (Qiagen). Poly-A mRNA was isolated and fragmented. First strand cDNA was prepared using reverse transcriptase and random hexamers. After second strand cDNA synthesis, ends were repaired and a single ‘A’ base was added followed by adapter sequences. Library fragments were selected for an average size of 200 to 260 base pairs, PCR amplified, and then sequenced using Illumina next-generation sequencing technology.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Low-quality bases as designated by CASAVA (v1.8) were trimmed from the 3' end of reads.
Reads were aligned using GSNAP (v2012-04-10). (Read length + 2)/12 – 2 or fewer mismatches were tolerated. Alignments to novel exon-exon junctions and known junctions as defined by RefSeq (downloaded March 7, 2011) and Gencode (v3c) were allowed. A list of SNPs in the CEU population from Hapmap (release #28) and 1000 Genomes (pilot project) was used to allow for SNP-tolerant alignments.
Variants were called with Samtools (v0.1.16)
Genome_build: hg18
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| Submission date |
Jul 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Isabel Xiaorong Wang |
| Organization name |
HHMI/University of Michigan
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| Department |
Pediatrics&Genetics
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| Lab |
Dr. Vivian G. Cheung Lab
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| Street address |
210 washtenaw ave
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| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE39167 |
Investigating the genetic basis of RNA Editing in humans |
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| Relations |
| SRA |
SRX158809 |
| BioSample |
SAMN01086571 |
| 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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