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| Status |
Public on Apr 01, 2020 |
| Title |
15CON |
| Sample type |
SRA |
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| Source name |
cerebral organoids
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| Organism |
Homo sapiens |
| Characteristics |
diagnosis: healthy control
cell type: Human iPSC derived cerebral organoids
state: 6 months of differention
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| Treatment protocol |
None
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| Growth protocol |
Lancaster protocol (https://www.nature.com/articles/nature12517)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample
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| Submission date |
Jul 18, 2019 |
| Last update date |
Apr 01, 2020 |
| Contact name |
Annie Kathuria |
| E-mail(s) |
kathu003@gmail.com
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| Organization name |
Mass Gen Hospital
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| Street address |
185 cambridge street
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE134497 |
Total RNA sequecing for human induced pluripotent derived cerebral organoids |
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| Relations |
| Alternative to |
GSM4188828 |
| BioSample |
SAMN12315348 |
| SRA |
SRX6466835 |
| 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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