 |
 |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 25, 2025 |
Title |
RNA-seq - LIS1+/- organoid day 105, repeat #4 |
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 |
SAMN34068636 |
SRA |
SRX19865497 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
 |