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Sample GSM4063577 Query DataSets for GSM4063577
Status Public on May 28, 2020
Title 02_353_Atg7KO-Low
Sample type RNA
 
Source name Atg7KO-Low
Organism Mus musculus
Characteristics genotype/variation: Atg7KO
cell type: CD24(low)/EGFP(Low) transit amplifying population
Treatment protocol Mice treated with tamoxifen for five consecutive days and sacrificed 1 month after treatment. Intestinal tissue was incubated in 15 mM EDTA in PBS for 25 minutes on ice then vigorously vortexed to release crypts. Crypts were dissociated by incubation in dispase buffer containing 0.3 U/ml dispase (Corning), 0.8 U/ml DNase (Ambion), 10 µM Y-27632 (Enzo) at 37°C for 30 min. Intestinal stem cells and their direct transit amplifying progenitors from individual mice were enriched by sorting CD24(low)/EGFP(High) or CD24(low)/EGFP(Low) populations, respectively.
Extracted molecule total RNA
Extraction protocol Cells were sorted directly into lysis buffer and RNA was extracted using the RNeasy Micro Kit (Qiagen).
Label biotin
Label protocol 1 ng of total RNA is reverse transcribed following the Ovation Pico System V2 (Tecan). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Tecan).
 
Hybridization protocol After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene2.0 ST (Affymetrix) at 45°C for 17 hours.
Scan protocol After overnight hybridization, chips are washed on the Fluidic Station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G.
Description Atg7KO sorted EGFP(Low) transit amplifying population.
Data processing The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.
RMA normalization is performed using R with Version 21 of EntrezGene CDF brainarray.
 
Submission date Sep 05, 2019
Last update date May 28, 2020
Contact name Franck Letourneur
E-mail(s) franck.letourneur@inserm.fr
Organization name INSERM
Department U1016
Lab genomic
Street address 22 rue mechain
City Paris
ZIP/Postal code 75014
Country France
 
Platform ID GPL23092
Series (1)
GSE136952 Autophagy maintains intestinal stem cell integrity

Data table header descriptions
ID_REF
VALUE Log2-RMA signal

Data table
ID_REF VALUE
100009600_at 3.6253
100009609_at 2.00851
100009614_at 3.58295
100009664_at 2.84185
100012_at 2.88749
100017_at 4.83845
100019_at 6.40339
100033459_at 2.46211
100034251_at 4.13562
100034675_at 2.69345
100034728_at 11.1285
100034729_at 3.27734
100034739_at 3.58902
100034748_at 3.69476
100036518_at 2.23139
100036520_at 6.03974
100036521_at 4.67321
100036523_at 5.93521
100036537_at 3.29089
100036768_at 4.97017

Total number of rows: 25429

Table truncated, full table size 439 Kbytes.




Supplementary file Size Download File type/resource
GSM4063577_02_353_Atg7KO-Low.CEL.gz 8.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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