|
| Status |
Public on Dec 31, 2021 |
| Title |
bulk_RNA-seq_PT1_day_16_replicate_2 |
| Sample type |
SRA |
| |
|
| Source name |
forebrain neural progenitors
|
| Organism |
Pan troglodytes |
| Characteristics |
time point: day_16
cell type: iPSC-derived forebrain neural progenitors
|
| Growth protocol |
iPS cells were differentiated into forebrain neural progenitor cells using the following protocol: The iPSCs were plated at 10.000 cells/cm2 in N2 medium (1:1 DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), 0.2% penicillin/streptomycin (Gibco)) with dual SMAD-inhibition (10 µM SB431542 (Axon), 100 ng/ml noggin (Miltenyi)) as well as ROCK inhibitor (10 µM Y27632) on LN111 coated Nunc delta surface multidishes (1.14 µg/cm2; Biolamina). The media was changed every 2-3 days to N2 medium with SMAD-inhibitors up until day 9 of differentiation when only N2 medium was used. On day 11 the cells were dissociated using StemPro accutase (75 µl/cm2; Gibco) and replated at 800,000 cells/cm2 on LN111-coated Nunc plates in B27 medium (Neurobasal supplemented with 1% B28 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin) supplemented with 10 µM ROCK inhibitor, BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2mM; Sigma-Aldrich). The cells were then harvested at day 13, 14, 15, or 16.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with RNeasy mini kit (Qiagen) for bulk RNA-seq
Libraries for bulk RNA-seq were prepared withTruSeq RNA Library prep kit v2 (Illumina). Single cell libraries were prepared with Chromium Single Cell 3' Library & Gel Bead kit v2 (10x Genomics)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt
pantro6.s2.multi.Gencode27.Exon.sjdb.v2.txt
|
| Data processing |
bcl2fastq (Illumina) was used for base-calling.
The reads were aligned to the genome (GRCh38 and PanTro6) using STAR aligner v2.5.0a, allowing for 0.03 mismatches per base and multimapping at up to 10 loci.
The Subread package FeatureCounts was used to quantify the reads overlapping Gencode v27 gene annotations. The human Gencode annotation was lifted over to PanTro6 using UCSC LiftOver tool.
single cell fastqs:
I1 Technical: Index read
R1 Technical: 16 bp Barcode and 10bp UMI
R2 Biological
Genome_build: GRCh38 and PanTro6
Supplementary_files_format_and_content: matrix.mat: raw read counts
Supplementary_files_format_and_content: Exon.sjdb.txt: featureCounts
|
| |
|
| Submission date |
Feb 27, 2019 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Johan Jakobsson |
| Organization name |
Lund University
|
| Lab |
Molecular Neurogenetics
|
| Street address |
Sölvegatan 17, building A11
|
| City |
Lund |
| ZIP/Postal code |
221 84 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL21121 |
| Series (1) |
| GSE127253 |
Post-transcriptional mechanisms distinguish human and chimpanzee forebrain progenitors |
|
| Relations |
| BioSample |
SAMN11027136 |
| SRA |
SRX5444594 |
