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Sample GSM4633828 Query DataSets for GSM4633828
Status Public on Jul 06, 2020
Title Gor d2 batch 1
Sample type SRA
 
Source name G1 gorilla iPS cell-derived organoids
Organism Gorilla gorilla
Characteristics time point: Day 2
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_d7_1903
RNA was isolated from ~300 G1 batch 1 organoids on day 2, cDNA libraries were barcoded with NEBNext indexing primers i704 and i502
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 SAMN15352038
SRA SRX8603251

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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