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| Status |
Public on Feb 23, 2019 |
| Title |
Molm13Combo rep1 |
| Sample type |
SRA |
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| Source name |
Molm13Combo
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Molm13
cell type: Acute Myeloid Leukemia(AML) cell line
treatment: TKI+GSI
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| Treatment protocol |
MV4-11 and MOLM-13 cells were treated in duplicate with DMSO, 2.5nM AC220, 25uM DAPT or 2.5nM AC220 plus 25uM DAPT (Combo) for 12h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected, washed with PBS, and then flash frozen on dry ice. We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution.
1)mRNA enrichment: Oligo dT Selection or rRNA depletion;2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer;3)End repair, add A tailing and adaptor ligation:The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments;4)PCR amplification:The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;6) Sequencing on BGISEQ-500 platform.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
online_YX software was used for basecalling
We use internal software SOAPnuke(version:v1.5.2) to filter reads, followed as: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases(N) are more than 10%; 3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read). After filtering, the remaining reads are called "Clean Reads" and stored in FASTQ format. We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts; HISAT2: Version: v2.0.4) to do the mapping step.
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step. HISAT2:ersion: v2.0.4. Parameters: -p 8 --phred64 --sensitive -I 1 -X 1000. Website: http://0-www-ccb-jhu-edu.brum.beds.ac.uk/software/hisat
We mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM. Bowtie2 :
Version: v2.2.5
Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 Website: http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml.RSEM : Version: v1.2.12 Parameters: default
Website: http://deweylab.biostat.wisc.edu/ RSEM
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Feb 22, 2019 |
| Last update date |
Feb 25, 2019 |
| Contact name |
Dan Li |
| E-mail(s) |
danli7172@hust.edu.cn
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| Organization name |
Tongji Hospital
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| Street address |
1095 Jie-Fang Avenue
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430030 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE126933 |
Combinatorial inhibition of Notch and FLT3 exerts synergistic cytotoxic effects in FLT3/ITD+ acute myeloid leukemia |
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| Relations |
| BioSample |
SAMN10987527 |
| SRA |
SRX5408206 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3618309_Molm13Combo1.gene.fpkm.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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