|
| Status |
Public on Jul 06, 2020 |
| Title |
Gor d10 batch 3 |
| Sample type |
SRA |
| |
|
| Source name |
G1 gorilla iPS cell-derived organoids
|
| Organism |
Gorilla gorilla |
| Characteristics |
time point: Day 10
|
| Growth protocol |
Human (H9) or Gorilla (G1) stem cells were used to generate brain organoids in Aggrewell 800 plates (StemCell Technologies) with 2000 cells per microwell. Organoids were cultured in and followed the timing of the STEMdiff Cerebral Organoid Kit protocol (StemCell Technologies, #08570) .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were flash-frozen in LN2 and stored at -80 °C. RNA from all 42 samples was purified in parallel directly from Trizol with the Direct-zol-96 RNA kit (Zymo Research).
cDNA libraries were generated according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760). cDNA was amplified for 12 cycles and barcoded with NEBNext Multiplex Oligos for Illumina (NEB #E7600). Samples were pooled together to 15 nM concentration and sequenced with single-end 50 base mode on 3 lanes of an Illumina HiSeq 4000 instrument.
bulk RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
GC_d15_2503
RNA was isolated from ~150 G1 batch 3 organoids on day 10, cDNA libraries were barcoded with NEBNext indexing primers i706 and i505
|
| Data processing |
Fastq files were trimmed using Trim Galore version 0.6.3_dev and Cutadpt version 2.4.
Human and gorilla reads were aligned to GRCh38 and Kamilah_GGO_v0 reference genomes respectively using HISAT2 (version 2.0.0-beta).
GTF gene annotation files for both of the reference genomes were downloaded and filtered for a list of 16,763 genes that are annotated with identical gene names in both species
Read counts were normalized to transcripts per million (TPM). Results can be found in hum_gor_combined_tpms_HISAT2.txt
Genome_build: GRCh38 or Kamilah_GGO_v0s
Supplementary_files_format_and_content: hum_gor_combined_tpms_HISAT2.txt contains TPM results for all samples as well as the mean and standard deviation for each condition.
|
| |
|
| Submission date |
Jun 23, 2020 |
| Last update date |
Jul 06, 2020 |
| Contact name |
Paula Freire Pritchett |
| E-mail(s) |
paulafp@mrc-lmb.cam.ac.uk
|
| Phone |
+44-(0)1223-267581
|
| Organization name |
Medical Research Council
|
| Street address |
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23656 |
| Series (1) |
| GSE153076 |
An early cell shape transition drives evolutionary expansion of human forebrain |
|
| Relations |
| BioSample |
SAMN15352044 |
| SRA |
SRX8603268 |
