|
| Status |
Public on Mar 22, 2023 |
| Title |
lL22_2 |
| Sample type |
SRA |
| |
|
| Source name |
colonoid, IL-22, replicate-2
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colonoid
strain: C57BL/6
treatment: IL-22
|
| Treatment protocol |
The mouse spheroids were stimulated with mouse recombinant IL-1b (100 ng/mL) and recombinant mouse IL-22 (1 ng/mL) for 12 hours.
|
| Growth protocol |
Mouse colons were dissected and and used to isolate crypts. Dispersed crypts were plated overnight in Matrigel with growth media (Advanced DMEM/F12, 2 mM GlutaMax, 10 mM HEPES, 100 U/ml penicillin, 100 μg/ml streptomycin, 1× N2 supplement, 1× B27 supplement) containing EGF (50 ng/ml), 20% L-WRN conditioned media.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using NanoDrop2000 for cDNA synthesis or Agilent Bioanalyzer 2100 before RNA-Seq Library preparation.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
colonoid, IL-22, replicate-2
|
| Data processing |
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed on CLC Genomics Workbench 7 (Qiagen).
The expression of the genes in all samples was calculated as Transcript Per Million mapped reads (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: .txt, raw counts matrix that contains all gene names and counts for each sample
|
| |
|
| Submission date |
Jan 07, 2022 |
| Last update date |
Mar 22, 2023 |
| Contact name |
Chandrashekhar Pasare |
| E-mail(s) |
Chandrashekhar.pasare@cchmc.org
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Immunology
|
| Lab |
Chandrashekhar Pasare
|
| Street address |
250 Albert Sabin Way
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE193267 |
IEC intrinsic IL-1R signaling holds dual roles in regulating intestinal homeostasis and inflammation |
|
| Relations |
| BioSample |
SAMN24730001 |
| SRA |
SRX13662901 |
