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| Status |
Public on Nov 01, 2020 |
| Title |
WT_day28-11 |
| Sample type |
SRA |
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| Source name |
human cerebral organoids, H9
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| Organism |
Homo sapiens |
| Characteristics |
time: day28
tissue: cerebral organoids
genotype: wild type
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNEasy
Lexogen Quantseq kit, UMI inclusion
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Data processing |
Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20).
Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1) .
Differential gene expression analysis on raw counts, and principal component analysis on variance stabilized, transformed count data were performed using DESeq2 v1.18.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts
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| Submission date |
May 28, 2020 |
| Last update date |
Nov 02, 2020 |
| Contact name |
Christopher Esk |
| Organization name |
IMBA - Institute of Molecular Biotechnology GmbH
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| Street address |
Dr. Bohr-Gasse 3
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL21697 |
| Series (2) |
| GSE151379 |
A human tissue screen identifies a regulator of ER secretion as a brain size determinant [RNA-Seq] |
| GSE151384 |
A human tissue screen identifies a regulator of ER secretion as a brain size determinant |
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| Relations |
| BioSample |
SAMN15048245 |
| SRA |
SRX8417783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4577035_WT_day28-11_counts.tsv.gz |
179.2 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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