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| Status |
Public on Apr 30, 2020 |
| Title |
0301hAstroC |
| Sample type |
SRA |
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| Source name |
iPSC astrocytes
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| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-derived astrocytes
cell line: SBAD-03-01
disease status: Ctrl
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA samples were prepared using standard poly-A isolation protocol (HiSeq 3000/4000 SBS Kit)
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Reference index was created based on the human transcriptome GRCh38 ensembl release 91 available through ensembl ftp (Homo_sapiens.GRCh38.cdna.all.fa.gz, Homo_sapiens.GRCh38.ncrna.fa.gz). Sequences in scafold chromosomes were removed before creating the reference index (keeping only chromosomes 1, 2, …, 22, X and Y). Transcript index was created with kallisto (version kallisto_linux-v0.43.1)
Kallisto was used by to estimate transcript abundances (counts per transcript). Version: kallisto_linux-v0.43.1
Gene annotations were obtained from the headers of the corresponding fasta files used to create the reference index.
Transcript abundances were summarized at the gene level using tximport R library
Genome_build: GRCh38 ensembl release 91
Supplementary_files_format_and_content: TAB delimited files contain ensembl transcript ID (target_id), transcript lenght (length), effective transcript length (eff_length) and estimated counts (est_counts) from kallisto
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| Submission date |
Apr 29, 2020 |
| Last update date |
Apr 30, 2020 |
| Contact name |
Jimena Monzón-Sandoval |
| E-mail(s) |
MonzonSandovalJ@cardiff.ac.uk
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| Organization name |
UK Dementia Research Institute at Cardiff University
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| Street address |
Maindy Road
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| City |
Cardiff |
| ZIP/Postal code |
CF24 4HQ |
| Country |
United Kingdom |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE149598 |
RNA-seq of iPSC-derived astrocytes that are capable of exerting pro-maturational effect on synaptic networks |
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| Relations |
| BioSample |
SAMN14771329 |
| SRA |
SRX8207667 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4505482_WTCHG_P180042_204155_counts.txt.gz |
2.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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