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Sample GSM7142935 Query DataSets for GSM7142935
Status Public on Jan 25, 2025
Title RNA-seq - LIS1+/- organoid day 105, repeat #2
Sample type SRA
 
Source name Cortical organoids
Organism Homo sapiens
Characteristics tissue: Cortical organoids
cell line: NIHhESC-10-0079 WIBR3
cell type: hESC
genotype: LIS1+/-
Treatment protocol Control and LIS1+/- brain organoids were either treated with MMP9 Catalytic domain for 10min at 37'c or with an equa volume of PBS (sham). RNA extraction followed the treatment.
Growth protocol hESCs were cultured in naïve media and then dissociated and aggregated in V-shaped low-adhesion wells. Days 0 -17: Dulbecco's Modified Eagle's Medium (DMEM), 20% KSR, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol, non-essential amino acids (NEAA) and Perstrep. 3uM SB-431542 and 5uM IWR-1 were freshly added. Days 18-35: aggregates moved to 10cm bacterial plates. The media used was DMEM-F12, Penstrep, Glutamax, and chemically defined lipid concentrate (CDLC). Days 35-70: B27 without vitamin A, 5ug/ml heparin, and N2 supplement were added to the media. Media was changed once in three days
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Direct-zol RNA Miniprep Plus kit (Zymo Research) following the manufacturer's protocols
Libraries were prepared using TrueSeq standard mRNA library kit NOVASeq6000, 100PE, 40~50m for mRNA and NEBNext Small RNA Prep Kit for small RNA
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing True SEQ Long RNA libraries were trimmed from their adapter with cutadapt and aligned to hg38 with STAR v2.5.2b
DEseq2 was applied to test for the differential expression between the conditions.
smallRNA libraries were also trimmed from the adapter with cutadapt, and ligned to the genome with STAR
using outFilterMatchNmin=16, alignSJDBoverhangMin=1000, alignIntronMax=1, alignEndsType EndToEnd, and outFilterMismatchNmax 3
The number of read count per gene was calculated with bedtools. The read count for mirRNAs that appear more than once in the genome was divided by the number of their copies in the genome.
Assembly: hg38
Supplementary files format and content: Supplementary_Table_2_RNAseq_CorticOs_D_105.xlsx,Supplementary_Table_3_SmallRNAseq_CorticOs_D105.xlsx,Supplementary_Table_5_RNAseq_brainOs_D_18_mmp9_treat.xlsx
Supplementary files format and content: raw read counts, normalized read count, DEseq2 statistics
 
Submission date Apr 04, 2023
Last update date Jan 25, 2025
Contact name Tsviya Olender
E-mail(s) tsviya.olender@weizmann.ac.il
Organization name The Weizmann Institute
Department Molecular Genetics
Street address 234 Herzl St.
City Rehovot
ZIP/Postal code 7610001
Country Israel
 
Platform ID GPL24676
Series (1)
GSE228926 How LIS1 is involved in the regulation of the extracellular matrix
Relations
BioSample SAMN34068638
SRA SRX19865495

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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